This survey of literature on substratumassociated microbiota from 2016 includes highlights of research findings associated with algae, cyanobacteria, and bacteria from a variety of aquatic environments, but primarily freshwaters. It covers topics of relevance to the Water Environment Federation along with those of emerging or recent interest such as nuisance, bloom forming and harmful algae, fossil fuel related contamination, and other environmental pollutants like nanoparticles. Additional interesting findings reported on include general ecology, method development, multistressor interactions, nutrient cycling, taxonomy and systematics, trophic interactions, and biomonitoring, bioassessment, and bioremediation.