Frustules are heterovalvar, that is, one valve possesses a raphe, while the other valve lacks a raphe. Species of Achnanthidium are generally small in size, with narrow valves (less than 30 µm in length and 5 µm in breadth). The shape of the valves differs by species, but the ends may be rounded, capitate or rostrate. In girdle view, the frustules appear arched. The raphe valve face is concave, while that of the rapheless valve is convex. The central area of the raphe valve may form a transverse fascia or subfascia. Terminal raphe fissures are usually present and may be highly deflected. The striae are usually uniseriate. An isolated row of narrow, elongate areolae are present on the mantle, separated from areolae on the valve face by a narrow hyaline area. Cells attach to substrata by a mucilaginous stalk or pad. In some species, sexual reproduction is similar to reproduction in Planothidium and Lemnicola.
Achnanthidium was originally described by Kützing, but it was subsumed into Achnanthes until the acceptance of more narrow taxonomic boundaries (Round et al. 1980, Kingston 2003). The genus is distinguished by striae morphology, frustule shape and growth habit. Common species in North America include A. minutissimum, A. rivulare, and A. deflexum. Like many marine Achnanthes, Achnanthidium typically attaches to benthic substrates by a mucilaginous stalk. Achnanthidium species often thrive in flowing waters, often dominating the communities of the high flow zones of rivers and wave zones of lakes. Some taxa are considered to be “oxygen loving” because they are found in turbulent, well-oxygenated water, however, cells may simply be more efficient at obtaining nutrients in such waters. Small cells such as Achnanthidium minutissimum (Kütz.) Czarnecki (= Achnanthes minutissima Kütz.) are physiologically more active than larger cells, due partly to their large surface to volume ratios.