A review of literature on substratrumassociated microbiotia from 2013 covers topics on benthic algae, bacteria and viruses from a range of aquatic environments, but focuses on freshwater ecosystems. Advances in laboratory, field, and assessment methods are highlighted as are updates in taxonomy and systematics. Aspects of water quality, waste‐water treatment, biofuels, nutrient cycling, food‐web interactions, land use changes, and environmental challenges such as climate change, pollutants, and impacts of medical substances are presented. our understanding of the ecology, taxonomy and assessment of substratum‐associated microbiota. In response to increased pressures from anthropogenic stressors and climate change on aquatic environments, researchers are re‐evaluating current knowledge and approaches to research, biomonitoring and assessment. In this review of the 2013 literature, advances in laboratory, field, and assessment methods are highlighted as are updates in taxonomy and systematics. A literature review of similar topics was completed in 2013 (Furey and Liess, 2013).