Over the last five decades, the Atlantic salmon Salmo salar has suffered marked population declines across its distribution, attributed inter alia to overfishing, barriers to migration, climate change, aquaculture, and pollution. Conservation measures have been implemented to protect and recover this species, but little improvement in its population status has been observed. Here, we used population monitoring data to estimate the abundance of Atlantic salmon originating from the River Frome in southern England. Subsequently, juvenile (parr-to-smolt) freshwater and adult marine (smolt-to-adult) survival estimates were used to understand associations with environmental and anthropogenic factors. Annual Atlantic salmon trapping and tagging data containing more than 148,000 juveniles were analysed from 2012 to 2024. Over the study period, juvenile freshwater survival varied without a significant temporal trend, whilst marine survival decreased. Annual juvenile freshwater survival rates ranged from 7.2% to 18.3% (mean 11.6%), with their between-year variation explained by mean winter river discharge (40%). In contrast, smolt-to-one- and two-sea-winter adult marine survival rates were significantly lower, varying between 0.4% and 6.1% (mean 2.2%). Sea ice extent within the Norwegian and Greenland Seas was the most important covariate that explained the greatest amount (60%) of variation in smolt-to-adult marine survival rates. Hitherto, Atlantic salmon conservation efforts have primarily focused on protecting juvenile life-stages in freshwater. This study revealed that smolt-to-adult marine survival was 81.6% lower than parr-to-smolt freshwater survival, so much greater emphasis should be given to understanding the factors affecting their mortality at sea to protect this important life-stage. At present, Atlantic salmon are afforded almost no protection at sea, unlike other threatened marine species, and despite population declines observed across their distribution. We discuss measures required to safeguard Atlantic salmon at sea.

Atlantic salmon (Salmo salar L.) populations in Scotland are subject to active management and conservation practices which require biological reference points (BRPs), specifically conservation limits, defined at the level of the stock. Acquiring the data necessary to independently derive these BRPs for all managed populations in Scotland is prohibitive, motivating the use of Bayesian hierarchical stock-recruitment models. These models provide a framework for the joint analysis of multiple monitored stocks, and the transportation of BRPs to non-monitored stocks. This framework was adapted to introduce nationally relevant and available covariates that might explain variation in recruitment dynamics among stocks and reduce uncertainty in posterior predictions of BRPs. Model selection was designed to maximise the prediction of BRPs for new stocks via leave-one-group-out cross-validation. Out-of-sample predictive performance was maximised by including information on latitude, land usage within the catchment and historic catch per area of salmon habitat in the model. The extensions to Bayesian hierarchical stock-recruitment methods presented here, when applied at a national scale, result in more locally discriminative posterior predictions compared to existing methods and are readily applicable to other stocks and species.

As habitat degradation threatens global biodiversity and conservation efforts are resource limited, maximising the effectiveness of habitat protection and thus restoration of wild populations is essential. For animals that occupy multiple habitats throughout their lifetime, understanding how the immediate (i.e., affecting a given life stage) and carry-over (i.e., affecting a subsequent life stage) effects of habitat quality impact their population dynamics could help prioritise effective habitat protection. Here, we use a bespoke integrated path analysis model that simultaneously accounts for effects of habitat characteristics, density-dependent regulation, and random effect structures, to draw inference from a case study dataset for the threatened diadromous fish, Atlantic salmon (Salmo salar). We show that higher quality growing habitat promotes greater young-of-year (YOY) body length by the end of the growing season that results in a subsequent higher probability of them surviving to be detected as seaward migrating juveniles. Further, these growing habitat characteristics, along with instream macrophyte cover, promote higher YOY abundance at the end of the growing season. Higher YOY abundance is associated with, on average, shorter YOY and a lower probability of subsequent survival, suggesting density-dependent processes are evident throughout these juvenile life stages. Our study demonstrates that detailed population and habitat monitoring data can be used to disentangle and quantify immediate and carry-over effects from myriad other regulatory processes. We postulate that such findings are useful to prioritise effective habitat management that maximises its beneficial (or minimises its detrimental) immediate and carry-over effects to different life stages of the target population.

Anadromous salmonids migrate seaward to exploit feeding and growth opportunities in marine habitats, yet how smolt biological characteristics influence their marine migratory behavior remains poorly understood. This study used 9 years of trout (Salmo trutta) population monitoring data from 15,595 tagged age-0+ parr, 1033 smolts detected migrating downstream in spring, and 99 adults detected returning from their first marine migration to the River Frome (Dorset, UK) to investigate the influence of smolt biological characteristics on their migration timing and maiden marine sojourn duration. Age-specific differences in the influence of smolt length on migration timing were found, with longer 1-year-old smolts emigrating later than their shorter counterparts within the same age class, but the opposite association existed for 2-year-old smolts. A bespoke integrated statistical model quantified the effects of smolt emigration day of year, age, sex, and length on the probability of first-time migrants returning to the river after one or more sea winters. Younger, later migrating smolts had a longer marine sojourn duration than their older, earlier migrating counterparts, and females remained at sea for longer periods than males. Although the statistical model was designed to maximize the use of information available in the data, it revealed only weak effects of smolt biological characteristics on the maiden marine sojourn duration. A complementary simulation study suggested that detecting more spring migrating smolts and analyzing longer time series of trout population monitoring data would increase the ability to detect statistically significant effects. Therefore, a strategic review of the trout population monitoring program, including more long-term biological data collection, is recommended. The modelling work presented here can provide guidance on the size of the required dataset and how to maximize the power of imperfect data.

For effective fishery management, estimated stock sizes, along with their uncertainties, should be accurate, precise, and unbiased. Atlantic salmon Salmo salar stock assessment in England and Wales (and elsewhere across the Atlantic) estimate returning salmon stocks by applying a measure of rod exploitation rate (RER), derived from less abundant fishery-independent stock estimates, to abundant fishery-dependent data. Currently, RER estimates are generated for individual principal salmon rivers based on available local data and assumptions. We propose a single, consistent, transparent, and statistically robust method to estimate salmon stocks that transfers strength of information from “data-rich” rivers, i.e. those with fisheries-independent data, to “data-poor” rivers without such data. We proposed, fitted, simplified, and then validated a Beta–Binomial model of RER, including covariates representing angler and fish behaviours, river flow, and random effects to control for nuisance effects. Our “best” model revealed covariate effects in line with our hypotheses and generalized to data not used to train it. We used this model to extrapolate stock estimates from 12 data-rich to 52 data-poor rivers, together with their uncertainties. The resulting river-specific salmon stock estimates were judged to be useful and can be used as key inputs to river-specific, national, and international salmon stock assessments.

Atlantic salmon Salmo salar is a socio-economically important anadromous fish species that has suffered synchronous population declines around the North Atlantic over the last five decades. Reduced marine survival has been implicated as a key driver of the declines, yet the relative importance of different stressors causing mortality at sea is not well understood. This review presents a synopsis of the principal stressors impacting Atlantic salmon in estuarine and marine environments. It also applies a semi-quantitative 2-D classification system to assess the relative effects of these stressors on English salmon stocks and their likely development over the next decade. Climate change and predation were identified as the biggest threats at present and over the next decade. Poor water quality and bycatch were classified as relatively high impact stressors, but with a lower likelihood of becoming more prevalent in the future due to available mitigation measures. Other, less influential, stressors included tidal barrages, artificial light at night, impingement in power-station cooling waters and thermal discharges, pile-driving noise pollution, invasive non-native species, electromagnetic fields, salmon mariculture, and tidal lagoons. Salmon fisheries exploitation was not regarded as an important stressor currently because effective exploitation rate controls have been implemented to substantially reduce fishing pressure. Future research priorities include addressing knowledge gaps on expanding stressor impacts from climate change, predation, renewable energy developments, and artificial light at night. Local management actions directed towards improving freshwater and estuarine habitats to maximise ecosystem resilience to stressors and minimise their cumulative impacts are recommended.

Coastal winds transport water masses and larval fish onshore or offshore which may influence estuarine recruitment, yet our understanding of the mechanism underlying this relationship is limited. Here, we combine datasets from a historical database of larval fish off southeast Australia with a high-resolution atmospheric reanalysis model to show that normalised abundance of coastally spawned larvae increased with weak to moderate upwelling favourable winds 14 days prior to sampling. The increase in abundance may reflect increased nutrient and plankton availability for larval fish. Normalised larval abundance decreased following strong upwelling favourable winds but increased after onshore (downwelling favourable) winds, due to wind-driven transport. By combining a commercial estuarine fisheries catch-rate dataset (4 species, 8 estuaries, 10 years) and the high-resolution atmospheric reanalysis model, we show that negative effects of upwelling favourable winds during the spawning period can be detected in lagged estuarine commercial fisheries catch rates (lagged by 2 – 8 years depending on species’ growth rates), potentially representing the same mechanism proposed for larval fish. Upwelling favourable winds in the southeast Australian region have increased since 1850 while onshore winds have decreased, which may reduce larval recruitment to estuaries. Coastal winds are likely an important factor for estuarine recruitment in the southeast Australian region and future research on the estuarine recruitment of fish should incorporate coastal winds.

Understanding salmonid discharge requirements can help inform management to conserve wild populations in a changing climate. This study developed Bayesian hierarchical mixed-effects models relating 0+ Atlantic salmon (Salmo salarL.) and trout (SalmotruttaL.) densities to different aspects of river discharge. Associations between these densities and nine hydrological variables representing the magnitude, frequency and duration of discharge events were evaluated using historical monitoring data from 36 sites on five rivers in England and Wales. All hydrological variables had weak associations with 0+ salmonid densities. More frequent high discharges between spawning and emergence were positively and negatively associated with 0+ salmon and trout densities, respectively. High discharges might increase spawning site availability for salmon and decrease egg-to-fry survival for trout. However, overall, only equivocal evidence was found regarding which discharge aspects affect juvenile salmonid densities. Therefore, a strategic review of juvenile salmonid monitoring programmes integrating environmental data collection is recommended.

Patterns in the Southern Oscillation Index (SOI) affect the life history of many aquatic organisms in the southern hemisphere. We examined the effect of this phenomenon and other factors (i.e. rainfall, river flow and sea surface temperature, SST) on the commercial harvest of the giant mud crab (Scylla serrata) in Australia, given the large inter-annual variations in the catch of this species over the last 15 years, particularly in the north. Regression models were applied to concurrent environmental and catch data for giant mud crab caught from 29 catchments that provided a combined harvest of >20 000 tonnes. Non-metric multidimensional scaling (nMDS) was also used to explore potential regional differences in catch trends. A combination of SOI, SST and rainfall/river flow explained 30–70% of the variability in commercial catches, with mean summer temperature being most influential at higher latitudes. The nMDS revealed distinct groupings of river systems that coincided with biogeographic regions. This work highlights the importance of climatic events on the harvest of giant mud crabs and reinforces the need to adopt a bioregional approach when assessing the performance of fisheries targeting this species.

Droughts are likely to increase in frequency and severity with climate change, modifying the economic viability of inshore fisheries in regions of hydrological extreme. Variation in the revenue and profit associated with different mixtures of fishing methods between non-drought and drought conditions was examined for commercial fishing businesses in three estuarine and coastal systems in eastern Australia from 1997 to 2007. Mean monthly revenue decreased from 8 to 36% between non-drought and drought. Decreased mean monthly revenue was primarily attributed to reduced revenue generation from ocean prawn trawling (≥20%) and estuarine prawn trawling (≥34%) during drought. Fishing method diversity (measured by a modified form of the Shannon index) and mean monthly revenue were positively related; however, mean monthly profit decreased between non-drought and drought under a range of alternative cost scenarios. Reduced mean monthly profit was primarily attributed to losses from ocean prawn trawling (≥15%) and estuarine prawn trawling (≥30%) during drought. Although diversified harvesting behaviour increased revenue generation, initial results indicated that this marginal economic benefit could have been compromised by the greater costs associated with the increased diversification which reduced overall profitability. Results of this analysis indicated that the commercial fishing sector is a drought-affected industry in New South Wales.

Multivariate patterns in commercial fisheries landings, effort and revenue from three adjacent estuarine and coastal systems were examined in eastern Australia between 9-month periods of flood (September 2000May 2001) and drought (September 2002May 2003). Patterns in species landings, methods of fishing effort and revenue per species were significantly different between flood and drought. Spearmans rank correlations between BrayCurtis similarity matrices for landings, effort and revenue indicated that patterns in fisheries metrics represented a mixed signal of ecological response and fishers harvesting behaviour. Flood and drought events were associated with shifts in the species composition of landings that were reciprocated between estuarine and coastal systems. Estuarine migrant species (e.g. school prawn Metapenaeus macleayi Haswell) primarily contributed to landings during flood, whilst marine estuarine-opportunist species (e.g. yellowfin bream Acanthopagrus australis Owen) primarily contributed to landings during drought. Flood and drought events redistributed fisheries resources between estuarine and coastal systems, modifying the bioeconomic productivity of commercial fisheries. Results indicated that flood and drought events influence commercial fisheries by modifying landings composition, fishers harvesting behaviour and revenue generation.

This review presents a synopsis of the impacts of freshwater flow on fisheries production in estuarine and coastal systems, with particular emphasis on regional examples from eastern Australia and southern Africa. Freshwater flow impacts habitat availability, trophic interactions, and fishers’ harvesting behavior in estuarine and coastal systems. Seasonal and interannual variation in freshwater flow influences the distribution and abundance of fish and invertebrates through changes in growth, survival, and recruitment. Episodic flood and drought events have pronounced impacts on fisheries production due to rapid changes in physicochemical conditions modifying species richness and diversity. Many documented reductions in fisheries production have been attributed to river regulation modifying natural variation in freshwater flow. Protecting natural flow regimes is likely to be an effective management strategy to maintain the production of estuarine and coastal fisheries. Understanding the freshwater requirements of estuarine and coastal fisheries will become increasingly important as climate change modifies the hydrological cycle and as human population growth increases demand for water resources. One major challenge for scientists seeking to explore relationships between freshwater flow and fisheries production is to understand how variable flows influence resource availability, fishing activity, and the economic performance of commercial fisheries in estuarine and coastal systems.

Commercial catch-per-unit-effort (CPUE) data from nine estuaries were related to hydrological variation in eastern Australia. Relationships between drought declaration, rainfall, freshwater flow and fisheries catch rates were assessed from 1997 to 2007. Estuaries varied from 0.5 to 2.0×106ML of mean freshwater inflow per annum. Monthly CPUE data from gillnetting were used to infer the abundance of yellowfin bream (Acanthropagrus australis), dusky flathead (Platycephalus fuscus), luderick (Girella tricuspidata), sand whiting (Sillago ciliata) and sea mullet (Mugil cephalus). CPUE for all species examined, except yellowfin bream, increased in proportion to freshwater flow and decreased during periods of drought. Freshwater flow may affect CPUE by stimulating migration and schooling due to salinity fluctuations altering habitat availability. Minimum and maximum flows were important determinants of CPUE. Freshwater flow per se may not be as important in influencing CPUE as extremes in the hydrological continuum. Seasonal flows were consistently the most important aspect of the flow regime that explained the highest proportion of variability in CPUE. Seasonal freshwater pulses proximate to critical reproductive periods may influence catchability by triggering seaward spawning migrations in estuarine-dependent fish.

Coastal winds transport larval fish towards the coast and estuaries where they ultimately recruit, yet our understanding of the mechanism of how different coastal winds interact to influence estuarine recruitment is incomplete. Here, we first demonstrate a two-stage recruitment mechanism showing that larvae of coastally spawned species increased in abundance with moderately strong upwelling favourable winds 14 days prior to sampling, reflecting increased nutrient and plankton availability for larval fish. The larvae of coastally spawned species increased in abundance with onshore (downwelling favourable) winds three days prior to sampling, which retain larvae near the coast, facilitating estuarine recruitment through onshore transport. Secondly, we show that effects of wind during the spawning period can be detected 2-8 years later (depending on the species) in estuarine commercial fisheries catch rates. Finally, we show in the southeast Australian region, upwelling favourable winds have increased while downwelling favourable winds have decreased since 1850, potentially reducing larval recruitment to estuaries. The two-stage wind mechanism identified in this study is likely applicable to other regions where wind driven upwelling occurs and influences onshore and offshore transport. Future research should incorporate coastal winds into predictions of estuarine catch rates.