Epithemia has an eccentric raphe system, positioned along the ventral margin. Each branch of the raphe is arched toward the dorsal margin. Externally, the proximal raphe slits terminate in expanded ends, while internally, the raphe slit is continuous through the central nodule. The raphe is also supported internally by large, transapical costae. The valvocopulum, which is the girdle band next to the valve mantle, often possesses septum-like extensions. Areolae are complex.
Living cells of Epithemia often possess endosymbiotic cyanobacteria capable of fixing atmospheric nitrogen. Species within the genus, therefore, are often tolerant of nitrogen limiting conditions. Epithemia is an exclusively freshwater genus. Cells are epiphytic and epipelic. They are commonly found in carbonate rich (alkaline) waters and can also tolerate relatively high conductivity.