Abstract. Methane (CH4) accumulates in bottom waters of lakes, however, the extent and drivers of inter-lake variation in bottom-water CH4 concentrations are poorly understood and have been studied mainly in northern lakes. This limits predictions of how bottom-water CH4 concentrations respond to warming and eutrophication in lakes, and how these changes might influence surface-water CH4 concentrations and, consequently, CH4 emissions. We report 168 measurements of paired bottom- and surface-water CH4 concentrations from 46 African lakes spanning a wide range of surface area (SA; 0.02–67,075 km²) and maximum depth (2–180 m). Bottom-water CH4 concentrations ranged from 7 to 5,608,382 nmol L⁻¹, spanning six orders of magnitude, and increased with increasing stratification, quantified from vertical density profiles using potential energy anomaly (PEA) and mixed layer depth (MLD), and inferred from NH₄⁺ concentrations or vertical conductivity gradients. Surface-water CH4 concentrations ranged from 7 to 168,114 nmol L⁻¹ and increased with both bottom-water CH4 concentrations and vertical stratification (positively related to PEA and negatively to MLD). The most strongly stratified lakes exhibited high bottom-water CH4 concentrations, resulting in enhanced vertical transfer of CH4 to surface waters despite lower vertical diffusion coefficients. In addition, these lakes had shallower mixed layers and therefore thinner oxygenated surface layers, likely reducing CH4 removal via methane oxidation. The positive relationship between both bottom- and surface-water CH4 concentrations and chlorophyll-a (Chl-a) has previously been interpreted as reflecting enhanced methanogenesis driven by phytoplankton-derived organic matter delivered to sediments. However, such relationships may be indirect and should be interpreted cautiously, as Chl-a was negatively related to MLD in our dataset, and both bottom- and surface-water CH4 concentrations were also negatively related to MLD. The ratio of surface to bottom CH4 concentrations (surface:bottom CH4 ratio) may indicate the relative increase in surface CH4 in response to increases in bottom CH4 driven by warming and eutrophication. This ratio was negatively related to bottom depth, PEA, and MLD, and positively related to bottom-water O2, indicating that the relative increase in surface-water CH4 with increasing bottom-water CH4 is greater in shallower, less stratified systems than in deeper, more stratified systems. Diffusive CH4 emission rates were highest in shallower, less stratified systems, where the response of surface-water CH4 to increases in bottom-water CH4 is expected to be greatest, as indicated by high surface:bottom CH4 ratios. We further tested whether surface-water CH4 concentrations scale with simple metrics in a dataset including highly stratified, small, and deep crater lakes with elevated hypolimnetic CH4. A multiple linear regression using SA and Chl-a explained ~51 % of the variance and appears suitable for upscaling dissolved CH4 concentrations. This approach could enable large-scale extrapolation of diffusive CH4 emissions using spatial datasets for SA and remotely sensed Chl-a.

Rivers are large natural sources of methane (CH4) resulting from the net balance of inputs from methanogenesis and removal by methane oxidation (MOX). Here, we use an extensive dataset collected from African and European rivers to investigate spatial patterns and causes of variability of MOX. The MOX rates were highest in African streams draining flooded forests and increased with river catchment size. In large rivers, MOX represented the more important pathway of dissolved in-stream CH4 removal compared to diffusive degassing to the atmosphere; but this relative share was minimal in small rivers and was, on average, higher in African streams (37%) than European streams (9%). The relationships between MOX rates and potential drivers such as total suspended matter, pH, or dissolved nutrient concentrations did not follow the patterns expected from controlled experiments reported in the literature and reflected the broad spatial patterns across and within the studied river networks driven by stream size and wetland connectivity.

Our understanding of the role of tropical lakes in regional carbon budgets remains hampered by a lack of data covering the vast diversity of lake types and settings. Here, we provide a first comprehensive survey of the carbon (C) biogeochemistry of the Lake Alaotra system, a large shallow lake (surface of 200 km2 and maximum depth of 2 m) surrounded by an extensive floodplain and rice fields located in the highlands of Madagascar. The current landscape in the region is grassland-dominated and dotted by major gullies called “lavaka”, which have historically been claimed to lead to high erosion rates and would, thus, also mobilize large amounts of soil C. We investigated the seasonal variability in the concentrations and stable isotope ratios of inorganic and organic C pools; moreover, we examined a range of other relevant proxies, including physicochemical parameters, dissolved CO2 and CH4 concentrations, total alkalinity, and chlorophyll a (Chl a) from spatially distributed sampling and seasonal monitoring of several rivers. While rivers were found to carry high total suspended matter (TSM) loads with a modest particulate organic C (POC) content, the lake itself and its outflow were characterized by much lower TSM values and a high relative contribution of POC to TSM (% POC). The POC concentration of the outflow (13.0±7.7 mg L−1) was substantially higher than in the inflowing water (1.9±2.1 mg L−1), and δ13C values were also distinct between inflowing water (-24.6±1.8 ‰) and the lake (-26.5±2.1 ‰) or its outflow (-25.2±1.4 ‰). Similarly, the lake outflow was surprisingly rich in dissolved organic carbon (DOC) (9.5±1.4 mg L−1) compared to inflowing water (2.6±1.1 mg L−1). This indicates that the lake and its surrounding wetlands act as a substantial source of additional organic C which is exported downstream. The CO2 and CH4 concentrations in inflowing and outflowing rivers were substantially higher than in lake waters, and they peaked during the rainy season due to lateral inputs from wetlands. However, sources of POC and DOC were uncoupled: δ13C data indicated that marsh vegetation was the main source of net DOC inputs, while phytoplankton contributed substantially to POC in the lacustrine waters, at least during parts of the sampling period. Indeed, lake suspended matter has relatively low POC / Chl a ratios (143–564, particularly during the May sampling period), high % POC (10 % to 29 %), and δ13C values (-26.5±2.1 ‰) distinct from those in marsh-derived organic matter. Despite the evidence for phytoplankton production as a contributor to the lake POC pool, the lake acted as a net source of CO2 to the atmosphere, likely due to the high C inputs from the surrounding marshes and to sediment respiration (considering the shallow water depth). Nevertheless, the partial pressure of CO2 (pCO2) levels in the surface waters of the lake were lower than those in the inflowing and outflowing rivers. This reduction is likely due to the combined effects of phytoplankton production, which assimilates CO2 during photosynthesis, and degassing processes. When CO2-supersaturated riverine water enters the open lake, increased turbulence caused by wind fetch enhances gas exchange with the atmosphere, allowing CO2 to escape more readily from the water column. The biogeochemical functioning of Lake Alaotra differs substantially from the large and deeper East African (sub)tropical lakes and is more similar to lakes surrounded by flooded forests in the Congo River basin, likely due to a combination of its large surface area and shallow water depth and the large extent of surrounding wetlands and floodplains. It acts as an abrupt element in the land–ocean continuum of the catchment, whereby the biogeochemical characteristics of the Maningory River (i.e. the lake outflow) are strongly determined by processes taking place in Lake Alaotra and its wetlands, rather than being reflective of characteristics and processes further upstream in the catchment.

Mangroves store significant amounts of carbon in both sediment and water. Methane (CH4) is often produced in anoxic, organic-rich sediments during carbon degradation and released to overlying waters via porewater exchange. Yet, a portion of CH4 can be oxidized to CO2 before emission. Here, we investigate whether CH4 oxidation impacts its emissions using high-temporal resolution CH4 concentration and stable isotope (delta C-13-CH4) observations collected over 14 tidal cycles in 2 Brazilian mangrove creeks with no river inputs. We found higher CH4 concentrations (similar to 150 nM) more depleted in C-13 (-75 parts per thousand) during low tide than high tide at both creeks. Similar delta C-13-CH4 values between low tide surface waters and porewaters further suggest tidally driven porewater exchange as the main source of CH4. More C-13-enriched CH4 in surface waters and surface sediments than deep sediments indicate partial CH4 oxidation prior to exchange with the atmosphere. A stable isotope mass balance revealed that 17-58% of CH4 was oxidized at rates of 3-25 mu mol m(-2) d(-1) in the water column of tidal creeks. A larger portion of deep porewater CH4 (45-61%) was oxidized in sediments prior to porewater exchange with surface creek waters. The two mangrove creeks had average water-air CH4 fluxes of 51-109 mu mol m(-2) d(-1) over spring-neap tidal cycles. These aquatic CH4 emissions offset only < 3% of the mangroves' soil carbon sequestration. Overall, CH4 oxidation in both surface water and sediment attenuated CH4 emissions to the atmosphere.

Abstract. The catchment of Lake Alaotra, a large shallow lake (surface is 200 km2, maximum depth 2 m) in the Malagasy highlands, is a region where the grassland dominated landscape is dotted by major gullies called “lavaka”, which has historically been claimed to lead to high erosion rates. Sedimentary archives in lakes such as Lake Alaotra could be of great help to resolve questions about the natural versus anthropogenic influences on the changing landscape, provided that we understand carbon sources and sinks within the lake, as well as the connection with the surrounding landscape through the input of material via inflowing water. Here, we provide a first comprehensive survey of the carbon (C) biogeochemistry of the Lake Alaotra system. We investigated the seasonal variability of the concentrations and stable isotope C ratios of inorganic and organic C pools, as well as a range of other relevant proxies, including physico-chemical parameters, dissolved CO2 and CH4 concentrations, total alkalinity, and Chl-a (chlorophyll a) from spatially distributed sampling and seasonal monitoring of several rivers. While rivers were found to carry high total suspended matter (TSM) loads with a modest particulate organic C (POC) content, the lake itself and its outflow were characterised by much lower TSM values and high %POC (relative contribution of POC to TSM). The POC concentration of the outflow (13.0 ± 7.7 mg L-1) was substantially higher than in the inflowing water (1.9 ± 2.1 mg L-1), and δ13C values were also distinct between inflowing water (-24.6 ± 1.8 ‰) and the lake (-26.5 ± 2.1 ‰) or its outflow (-25.2 ± 1.4 ‰). Similarly, the lake outflow was surprisingly rich in DOC (9.5 ± 1.4 mg L-1) compared to inflowing water (2.6 ± 1.1 mg L-1). This indicates that the lake and its surrounding wetlands act as a substantial source of additional organic C which is exported downstream. The CO2 and CH4 concentrations in inflowing and outflowing rivers were substantially higher than in lake waters, and peaked during the rainy season due to lateral inputs from wetlands. However, sources of POC and DOC were uncoupled: δ13C data were consistent with marsh vegetation being the main source of net DOC inputs, while phytoplankton was expected to be an important source of POC in the lacustrine waters. Lake suspended matter has low POC/Chl-a ratios (143–564), high %POC (10 to 29 %), and δ13C values around 20 ‰ lower than the dissolved inorganic C (DIC) pool (-26.5 ± 2.1 ‰ versus -6.7 ± 1.6 ‰). Despite the importance of phytoplankton production to the lake POC pool, the lake acted as a net source of CO2 to the atmosphere, likely due to the high C inputs from the surrounding marshes, and sediment respiration considering the shallow water depth. Nevertheless, the pCO2 in the surface waters of the lake was lower than in the inflowing and outflowing rivers, possibly reflecting the impact of phytoplankton production (CO2 assimilation), although also reflecting degassing to the atmosphere. The biogeochemical functioning of Lake Alaotra differs substantially from the large and deeper East African (sub)tropical lakes and was similar to lakes surrounded by flooded forest in the Congo River basin, likely due to a combination of its large surface area and shallow water depth, and the large extent of surrounding wetlands and floodplains. It acts as an abrupt element in the land-ocean gradient of the catchment, whereby the biogeochemical characteristics of the Maningory River (i.e., the lake outflow) are strongly determined by processes taking place in Lake Alaotra and its wetlands, rather than being reflective of characteristics and processes higher up in the catchment.

We report dissolved CO2, CH4 and N2O concentrations in two large East African lakes, Edward (surface area 2,325 km2, average depth of 37 m) and George (surface area 273 km2, average depth of 2 m). Lake George showed modest seasonal and spatial variations, and lower partial pressure of CO2 (pCO2) (26 & PLUSMN; 16 ppm, mean & PLUSMN; standard deviation), CH4 (234 & PLUSMN; 208 nmol/L) and N2O saturation levels (%N2O) (80 & PLUSMN; 9 %) than Lake Edward (404 & PLUSMN; 145 ppm, 357 & PLUSMN; 483 nmol/L, 139 & PLUSMN; 222 %). Surface waters in both lakes were over-saturated in CH4, and Lake George was under-saturated in CO2 while Lake Edward was slightly over-saturated in CO2. This difference was related to higher phytoplankton biomass in Lake George than Lake Edward, with average chlorophyll-a concentrations of 177 & PLUSMN; 125 and 18 & PLUSMN; 25 lg/L, respectively. Permanent high cyanobacterial biomass in Lake George led to uniform dissolved CO2, CH4 and N2O concentrations. In surface waters of Lake Edward, spatial variations of pCO2, CH4 and N2O were related to bottom depth, and locally (in particular in Katwe Bay) also related to the inputs of water from Lake George via the Kazinga Channel, a 40-km natural channel connecting the lakes. Short-term mixing events related to storms increased CO2, CH4 and N2O content in surface waters, in particular for CH4 and N2O. This indicates that mixing events in response to storms can create 'hot moments' for CH4 and N2O emissions to the atmosphere in tropical lakes, given the weaker vertical density gradients compared to higher latitude systems.& COPY; 2022 International Association for Great Lakes Research. Published by Elsevier B.V. All rights reserved.

Geo-referenced and timestamped data-set of water temperature, Specific conductivity (SpCond), oxygen saturation level (%O2), dissolved methane (CH4) concentration, dissolved nitrous oxide (N2O) concentration, partial pressure of carbon dioxide (pCO2), carbon stable isotope composition of dissolved inorganic carbon (δ13C-DIC), dissolved organic carbon (DOC) concentration, chlorophyll-a (Chl-a) concentration, cyanobacteria abundance (CHEMTAX), nitrate (NO3-) and ammonia concentration (NH4+), coloured dissolved organic matter slope ratio (CDOM SR) in surface waters of African 24 lakes (Victoria, Tanganyika, Albert, Kivu, Edward, Mai Ndombe, Tumba, George, Kamohonjo, Alaotra, Ndalaga, Nyamusingere, Kyamwinga, Mbita, Lukulu, Yandja, Mbalukira, Nkugute, Nyamunuka, Kitagata, Mrambi, Kyashanduka, Katinda, Lac Vert).

Heterotrophic respiration of organic matter (OM) is thought to dominate over aquatic primary production (PP) in most freshwater lake ecosystems. This paradigm implies that lateral transport of OM from the terrestrial biosphere subsidize the major fraction of aquatic respiration and that many lakes are a net source of carbon dioxide (CO 2 ) to atmosphere. Nevertheless, African lakes were absent of the datasets upon which this paradigm was built. Here, we report a comprehensive and methodologically consistent data set of pelagic PP and community respiration (CR) obtained over the last decade in contrasting non-humic African lakes including 5 of the East African Great lakes (Tanganyika, Kivu, Edward, Albert, Victoria) and smaller shallow lakes located in Eastern Africa. Also, we determined the partial pressure of CO 2 in surface waters and examined the sources and dynamics of organic and inorganic carbon by means of stable isotope tools across a wide range of physical and chemical conditions and productivity status. Our observations revealed that the threshold value at which the equivalence between PP and CR is met is substantially lower in Africa (10 mmol C m −3 d −1 ) than at higher latitude (25 mmol C m −3 d −1 ), suggesting that non-humic African lakes tend to be more autotrophic than expected from empirical relationships derived from data collected in boreal and temperate regions. Integrated at the regional scale, we estimate that PP is about 20 times higher than the organic carbon burial in sediments. It implies that a large fraction (< 90%) of PP is effectively recycled in the warm water column of non-humic African lakes.

Natural lakes are thought to be globally important sources of greenhouse gases (CO2, CH4, and N2O) to the atmosphere although nearly no data have been previously reported from Africa. We collected CO2, CH4, and N2O data in 24 African lakes that accounted for 49% of total lacustrine surface area of the African continent and covered a wide range of morphology and productivity. The surface water concentrations of dissolved CO2 were much lower than values attributed in current literature to tropical lakes and lower than in boreal systems because of a higher productivity. In contrast, surface water-dissolved CH4 concentrations were generally higher than in boreal systems. The lowest CO2 and the highest CH4 concentrations were observed in the more shallow and productive lakes. Emissions of CO2 may likely have been substantially overestimated by a factor between 9 and 18 in African lakes and between 6 and 26 in pan-tropical lakes.

ABSTRACT East African Great Lakes are old and unique natural resources heavily utilized by their bordering countries. In those lakes, ecosystem functioning is dominated by pelagic processes, where microorganisms are key components; however, protistan diversity is barely known. We investigated the community composition of small eukaryotes (<10 µm) in surface waters of four African Lakes (Kivu, Edward, Albert and Victoria) by sequencing the 18S rRNA gene. Moreover, in the meromictic Lake Kivu, two stations were vertically studied. We found high protistan diversity distributed in 779 operational taxonomic units (OTUs), spanning in 11 high-rank lineages, being Alveolata (31%), Opisthokonta (20%) and Stramenopiles (17%) the most represented supergroups. Surface protistan assemblages were associated with conductivity and productivity gradients, whereas depth had a strong effect on protistan community in Kivu, with higher contribution of heterotrophic organisms. Approximately 40% of OTUs had low similarity (<90%) with reported sequences in public databases; these were mostly coming from deep anoxic waters of Kivu, suggesting a high extent of novel diversity. We also detected several taxa so far considered exclusive of marine ecosystems. Our results unveiled a complex and largely undescribed protistan community, in which several lineages have adapted to different niches after crossing the salinity boundary.

While the emissions of methane (CH4) by natural systems have been widely investigated, CH4 aquatic sinks are still poorly constrained. Here, we investigated the CH4 cycle and its interactions with nitrogen (N), iron (Fe) and manganese (Mn) cycles in the oxic-anoxic interface and deep anoxic waters of a small, meromictic and eutrophic lake, during two summertime sampling campaigns. Anaerobic CH4 oxidation (AOM) was measured from the temporal decrease of CH4 concentrations, with the addition of three potential electron acceptors (NO3-, iron oxides (Fe(OH)(3)) and manganese oxides (MnO2)). Experiments with the addition of either N-15-labeled nitrate (N-15-NO3-) or N-15-NO3- combined with sulfide (H2S), to measure denitrification, chemolithotrophic denitrification and anaerobic ammonium oxidation (anammox) rates, were also performed. Measurements showed AOM rates up to 3.8 mu mol CH4 L-1 d(-1) that strongly increased with the addition of NO3- and moderately increased with the addition of Fe(OH)(3). No stimulation was observed with MnO2 added. Potential denitrification and anammox rates up to 63 and 0.27 mu mol N-2 L-1 d(-1), respectively, were measured when only N-15-NO3- was added. When H2S was added, both denitrification and anammox rates increased. Altogether, these results suggest that prokaryote communities in the redoxcline are able to efficiently use the most available substrates.

In the ferruginous and anoxic early Earth oceans, photoferrotrophy drove most of the biological production before the advent of oxygenic photosynthesis, but its association with ferric iron (Fe3+) dependent anaerobic methane (CH4) oxidation (AOM) has been poorly investigated. We studied AOM in Kabuno Bay, a modern analogue to the Archean Ocean (anoxic bottom waters and dissolved Fe concentrations > 600 µmol L−1). Aerobic and anaerobic CH4 oxidation rates up to 0.12 ± 0.03 and 51 ± 1 µmol L−1 d−1, respectively, were put in evidence. In the Fe oxidation–reduction zone, we observed high concentration of Bacteriochlorophyll e (biomarker of the anoxygenic photoautotrophs), which co-occurred with the maximum CH4 oxidation peaks, and a high abundance of Candidatus Methanoperedens, which can couple AOM to Fe3+ reduction. In addition, comparison of measured CH4 oxidation rates with electron acceptor fluxes suggest that AOM could mainly rely on Fe3+ produced by photoferrotrophs. Further experiments specifically targeted to investigate the interactions between photoferrotrophs and AOM would be of considerable interest. Indeed, ferric Fe3+-driven AOM has been poorly envisaged as a possible metabolic process in the Archean ocean, but this can potentially change the conceptualization and modelling of metabolic and geochemical processes controlling climate conditions in the Early Earth.

Lake Victoria experienced a strong degradation of water quality between the 1960s and the 1990s and, as a consequence of eutrophication, the dominant phytoplankton group changed from diatoms to N-2-fixing cyanobacteria and there was a 2- to 10-fold increase in chlorophyll-a. The goal of this study is to determine whether the 2018-2019 physical (light, stratification) and ecological (nutrient, chlorophyll-a, phytoplankton composition) conditions in Lake Victoria changed from the 1990s. Samples were collected in 2018-2019 in nearshore and offshore waters (Uganda), during three contrasting seasons: heavy rains (March), low rains (October), and dry (June), which corresponded to distinct water column mixing regimes, respectively, late-stratified, early-stratified, and mixed regimes. At each station (48 nearshore and 25 offshore), we measured vertical profiles of temperature, oxygen, phytoplankton biomass and composition, inorganic nutrients, and particulate organic carbon, particulate nitrogen (N), and phosphorus (P). Chlorophyll-a concentrations in 2018-2019 were 10.3 +/- 7.1 and 2.8 +/- 1.1 mu g/L in the nearshore and offshore surface waters, respectively, close to those measured in the 1960s before eutrophication, but distinctly lower than those measured in the 1990s (71 +/- 100 and 14 +/- 6 mu g/L). The phytoplankton of Lake Victoria in 2018-2019 still appears dominated by diatoms and cyanobacteria. However, we observed more non-heterocystous filamentous and coccal/colonial cyanobacteria taxa that are better adapted to mixing conditions than gas-vacuolated heterocystous taxa, which were dominant in the 1990s. Particulate N was significantly lower in 2018-2019 than in the 1990s, indicative of less efficient N fixation. The dissolved silica concentrations in 2018-2019 were significantly higher with the concomitant reappearance of Aulacoseira spp., which was not observed in the 1990s, presumably due to low dissolved silica concentrations. As data from long-term monitoring are absent, the reasons for the lower chlorophyll-a concentrations in 2018-2019 compared to the 1990s are unclear. However, climatic controls (El Nino/La Nina conditions) may be an important factor influencing the historical trend in chlorophyll-a. Higher wind in 2018-2019 promoted vertical mixing, resulting in a deeper thermocline and surface mixed layers, which eventually lowered phytoplankton production in comparison to the 1990s. In contrast, the thermocline and surface mixed layers in the 1990s were shallower, enabling phytoplankton to stay suspended in the upper well illuminated water, allowing greater productivity. The lake in 2018-2019 is still P saturated, suggesting that another episode of high chlorophyll-a concentrations could develop if less windy conditions occur in future, or if continued warming of surface waters eventually overcomes the mixing from present windy conditions. This study gives insights about the present ecological functioning of Lake Victoria and emphasises the impacts of variations in climate on lake physics that changes the light environment for phytoplankton. A possible less windy period in the future resulting from a new El Nino phase or from climate change, will probably lead to another episode of eutrophication in Lake Victoria. As in 2018-2019 the lake was still saturated by nutrients, there is need to reduce the nutrient concentrations (especially P) to prevent future destructive eutrophic periods caused by reduced mixing.

Aquifers under agricultural areas are considered to be an indirect source of nitrous oxide emission (N2O) to the atmosphere, which is the greenhouse gas (GHGs) characterized with the highest global warning potential and acts as a stratospheric ozone depletion agent. Previous investigations performed in the Cretaceous Hesbaye chalk aquifer in Eastern Belgium suggested that the dynamics of N2O in the aquifer is controlled by overlapping biochemical processes such as nitrification and denitrification. The current study aims to obtain better insight concerning the factors controlling the distribution of N2O concentration along a vertical dimension in the aquifer, and to capture and quantify the occurrence of nitrification and denitrification processes in the groundwater system. Low-flow groundwater sampling technique was undertaken at different depths in the aquifer to collect groundwater samples aiming at obtaining information about ambient aquifer hydrogeochemical conditions and their effect on the accumulation of GHGs. Afterwards, laboratory stable isotope experiments, using NO3- and NH4+ compounds labeled with heavy 15N isotope, were applied to quantify the rates of nitrification and denitrification processes. Ambient studies suggest that the occurrence of N transformation was related to denitrification while laboratory incubation experiments did not detect it. Such controversial results might be explained by the discrepancy between real aquifer conditions and lab design studies. Thus, additional in situ tracer experiments should be carried out in areas where natural groundwater fluxes do not flush the injected tracer too rapidly. In addition, it would be useful to conduct microbiological studies to obtain better insight into the nature of subsurface biofilm biotope.

Lake Edward is one of the African Rift Valley lakes draining into the Nile River basin. We conducted three sampling series in Lake Edward in October-November 2016, March-April 2017 and January 2018, in distinct seasonal conditions and in several sites varying by depth and proximity to river outlets, including the Kazinga Channel, which connects the hypertrophic Lake George to Lake Edward. The phytoplankton was examined using microscopy and marker pigment analysis by high performance liquid chromatography (HPLC) and subsequent CHEMTAX processing for estimating abundance of phytoplankton groups. Chlorophyll a concentration in the pelagic and littoral open lake sites barely exceeded 10 mu g L-1 whereas, in contrast, in the semi-enclosed Bay of Katwe influenced by the Kazinga Channel chlorophyll a was up to 100 mu g L-1. Despite substantial seasonal variations of limnological conditions such as photic and mixed layer depths, cyanoprokaryotes/cyanobacteria represented on average 60% of the phytoplankton biomass, followed by diatoms, which contributed similar to 25% of chlorophyll a, and by green algae, chrysophytes and cryptophytes. 248 taxa were identified with clear prevalence of cyanobacteria (104 taxa), from the morphological groups of coccal and filamentous species (non-heterocytous and heterocytous). The high proportion of heterocytous cyanobacteria, along with a relatively high particulate organic carbon to nitrogen (C:N) ratio, suggest N limitation as well as light limitation, most pronounced in the pelagic sites. During the rainy season, the most abundant diatoms in the plankton were needle-like Nitzschia. Comparison with previous studies found differences in water transparency, total phosphorus, and phytoplankton composition. (C) 2020 International Association for Great Lakes Research. Published by Elsevier B.V. All rights reserved.