Epipelic microphototrophs perform a range of ecosystem functions including biostabilization of sediments, regulation of benthic—limnetic nutrient cycling, and primary production. This review summarizes the most recent research of lake/pond phototrophic epipelic taxa and highlights the importance of an approach to identifying these algae that combines classic and modern methods, particularly metagenomics and sequencing. The contribution of true epipelic chlorophyll a concentration to total sediment chlorophyll a production can reach 30%, particularly at sites of intermediate depth. Autochthonous epipelic assemblages (diatoms, cyanobacteria, desmids, and euglenophytes) are highly diverse, but overlooked. The result has been recent erection of new genera and species. Species distribution seems to follow ecological gradients (pH, conductivity, trophy) and can be used in biomonitoring.