A review of literature on substratrum-associated 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.