This review summarises knowledge on the ecology, toxin production, and impacts of toxic freshwater benthic cyanobacterial proliferations. It documents monitoring, management, and sampling strategies, and explores mitigation options. Toxic proliferations of freshwater benthic cyanobacteria (taxa that grow attached to substrates) occur in streams, rivers, lakes, and thermal and meltwater ponds, and have been reported in 19 countries. Anatoxin‐ and microcystin‐containing mats are most commonly reported (eight and 10 countries, respectively). Studies exploring factors that promote toxic benthic cyanobacterial proliferations are limited to a few species and habitats. There is a hierarchy of importance in environmental and biological factors that regulate proliferations with variables such as flow (rivers), fine sediment deposition, nutrients, associated microbes, and grazing identified as key drivers. Regulating factors differ among colonisation, expansion, and dispersal phases. New ‐omics‐based approaches are providing novel insights into the physiological attributes of benthic cyanobacteria and the role of associated microorganisms in facilitating their proliferation. Proliferations are commonly comprised of both toxic and non‐toxic strains, and the relative proportion of these is the key factor contributing to the overall toxin content of each mat. While these events are becoming more commonly reported globally, we currently lack standardised approaches to detect, monitor, and manage this emerging health issue. To solve these critical gaps, global collaborations are needed to facilitate the rapid transfer of knowledge and promote the development of standardised techniques that can be applied to diverse habitats and species, and ultimately lead to improved management.

Aquaculture is an extremely valuable and rapidly expanding sector of the seafood industry. The sediment below active aquaculture farms receives inputs of organic matter from uneaten food and faecal material and this has led to concerns related to environmental sustainability. The impacts of organic enrichment on macrobenthic infauna are well characterized; however, much less is known about effect on bacterial communities. In this study, sediment, macrobenthic infauna samples and environmental data were collected along an enrichment gradient radiating out from a Chinook salmon (Oncorhynchus tshawytscha) farm (Marlborough Sounds; New Zealand). DNA and RNA were extracted and 16S rRNA metabarcodes from bacterial communities characterized using high-throughput sequencing. Desulfobacterales dominated at the cage (DNA and RNA), and at sites 50 m (DNA and RNA) and 150 m (RNA) from the farm. In contrast, unclassified bacteria from the class Gammaproteobacteria were the most abundant taxa at control sites (625 and 4000 m). Pronounced differences among DNA and RNA samples occurred at the cage site where Desulfobacterales abundance was markedly higher in RNA samples. There were strong correlations between shifts in bacterial communities and total organic matter and redox. This suggests that bacterial composition is strongly influenced by organic enrichment, a trait that may make them useful for assessing impacts associated with aquaculture farms.