This survey of 2018 literature on substratum‐associated microbiota presents brief highlights on research findings from primarily freshwaters, but includes those froma variety of aquatic ecosystems. Coverage of topics associated with benthic algae andcyanobacteria, though not comprehensive, includes new methods, taxa new to science, nutrient dynamics, trophic interactions, herbicides and other pollutants, metalcontaminants, nuisance, bloom‐forming and harmful algae, bioassessment, andbioremediation. Coverage of bacteria, also not comprehensive, focused on methylation of mercury, metal contamination, toxins, and other environmental pollutants, including oil, as well as the use of benthic bacteria as bioindicators, in bioassessment tools and in biomonitoring. Additionally, we cover trends in recent and emerging topics on substratum‐associated microbiota of relevance to the Water Environment Federation. © 2019 Water Environment Federation.