Increased delivery of sediment and nutrients from the land threatens the health and productivity of key ecosystems of the Great Barrier Reef (GBR) lagoon. This chapter is an update to the Furnas and Mitchell (2000) "Runoff of terrestrial sediment and nutrients into the Great Barrier Reef World Heritage Area" chapter from the first edition and incorporates our latest understanding of GBR catchment sediment and nutrient generation processes, transport, and transformations. We provide a review of the history of monitoring and research in the GBR Catchment Area (GBRCA) that has led to improved estimates of sediment and nutrient loads and how it has changed over time under catchment development. This includes targeted monitoring, tracing, and modelling approaches and proxy-based evidence within both the catchment and lagoon. This review emphasises the increasing use of the latest high temporal frequency, near real time sensor technologies to capture the complexity of hydrology, sediment, and nutrient runoff at small-scale tributary sites, including the highly elevated concentrations associated with the first-flush runoff. We present the latest 'best available' load estimates from each of the 35 basins of the GBRCA for fine sediment (< 20 µm fraction), particulate nitrogen and phosphorus, and dissolved inorganic nitrogen. Finally, we consider the available management options to reduce the loads of sediment and nutrients delivered to the GBR lagoon that include policy instruments.

Concentrations of a range of pesticides exceed water-quality guidelines throughout the year in many fresh and estuarine water bodies of the Great Barrier Reef catchment. To mitigate its impact and maintain its productivity, the Australian sugar industry is looking at innovative options to reduce the movement of herbicides off site. Three oil-based adjuvants (Grounded (R) applied at 3 L/ha, Atpolan (R) soil Maxx applied at 0.4 L/ha and Ad-HereTM applied at 1L/ha according to their respective labels), a terpene-based adjuvant (Flextend (R) applied at 1.2 L/ha) and a polyol-based adjuvant (Watermaxx (R) 2 applied at 9.35 L/ha), were tested on bare soil and on a trash blanket for their potential to reduce runoff losses as well as improving the weed control efficacy of four registered pre-emergent herbicides applied at full label rate: imazapic (96 g/ha), hexazinone (975 g/ha), isoxaflutole (150 g/ha) and amicarbazone (700 g/ha). Herbicide-efficacy trials were implemented as randomised complete-blocks with three replicates and adjacent untreated controls. Losses of the tested pre-emergent herbicides in runoff were monitored using replicated rainfall simulations, delivering 80 mm of simulated rain, 48 h or 3 weeks after herbicide application. On green-cane trash-blanket, all oil-based adjuvants significantly increased the runoff of the tested herbicides, Flextend did not affect herbicide runoff and Watermaxx2 slightly reduced herbicide concentration in runoff by up to 25%. On bare soil, three of the tested adjuvants significantly reduced herbicide runoff losses. Grounded achieved the best outcomes by reducing herbicide concentration in runoff by about 35% when runoff occurred 48 h after application. Most of the tested products slightly increased herbicide efficacy on weeds in the efficacy trials, but the differences were not significant. If validated in other soil types and in bare soil ratoon cane, the use of Grounded (R)Psi could assist in improving the quality of runoff water leaving sugarcane paddocks and, therefore, reduce canegrowers impact on freshwater water and marine ecosystems.

Imidacloprid represents the Australian sugar industry’s best canegrub-management tool, but it has been detected in many water bodies, including groundwater, creeks, rivers and marine environments, posing a potential risk to the health of the Great Barrier Reef. In ratoon cane, it is commonly applied in liquid form with coulters within the cane row. Imidacloprid product labels state that, when applied in ratoons, the product must be placed at 100–125 mm depth and the slot must be covered; however, it is not uncommon to observe application equipment that does not maintain the desired depth or fails to close the slot appropriately. To investigate the best application methods to reduce imidacloprid runoff, two rainfall-simulation trials were established in the Burdekin and in the Wet Tropics to assess the impact of depth and slot coverage on imidacloprid runoff when the liquid formulation is applied with a stool-splitter tine implement. An additional runoff trial under overhead irrigation was set up in the Wet Tropics to test the efficacy of the StoolZippaTM to close the slot and reduce imidacloprid runoff losses when the product is applied at the correct depth of 100 mm. Results from the rainfall-simulation trials showed higher imidacloprid concentration in runoff from a shallow application at 50 mm compared to the recommended minimum 100 mm application depth. A press wheel reduced the imidacloprid concentration to nil when the product was applied at the correct depth of 100 mm; however, it slightly increased the concentration in the case of the shallow application. In the overhead-irrigation trial, the StoolZippaTM increased the imidacloprid concentrations in runoff versus the slot left open, but these concentrations were still extremely low and not of environmental concern. These trials indicate that ensuring the product is consistently applied at 100 mm depth is the best way to reduce imidacloprid loss via runoff when the product is applied with a stool-splitter tine implement. As trials were only conducted in loam soils at two locations, further trials are recommended over a range of soil types and geographic locations.

Contrasting evolutionary histories may be revealed by mitochondrial and nuclear information. Divergent New Guinean and eastern and western Australian lineages of Hephaestus fuliginosus (sooty grunter) were detected using mitochondrial data, with the extent of divergence consistent with cryptic speciation events. However, this phylogeographic pattern was not supported by nuclear gene data, and evidence for cryptic speciation appears driven almost entirely by introgression between H. fuliginosus and congeners on the periphery of its distribution (e.g. with H. tulliensis, H. jenkinsi or H. roemeri). Hephaestus fuliginosus is a single species with a complex evolutionary history. Introgression on the eastern coast is consistent with transfer of the mitochondrial genome of the resident species (H. tulliensis) to the invading species (H. fuliginosus) and may have provided the metabolic capacity for H. fuliginosus to spread into the cooler rainforest environment of the Wet Tropics region. Mitochondrial and nuclear analyses both identified the genus Hephaestus as polyphyletic with H. carbo and H. habbemai placed in a clade with Leiopotherapon unicolor and Amniataba percoides. The present study demonstrated the need to consider a variety of genetic information when assessing species identity in a widespread species and the need for a systematic revision of the genus and family as a whole.