Cocconeis is heterovalvar, that is, the raphe valve ornamentation differs from that of the rapheless valve. Ornamentation of the raphe valve may differ markedly from that of the rapheless valve. The valve mantle is narrow in relation to the valve face, so cells are rarely (if ever) seen in girdle view. Valves may be flexed, or arched, along the apical axis forming a 'saddle' shape. Striae are often uniseriate, but some taxa possess multiseriate striae composed of loculate areolae. In several taxa, the raphe valve is marked by a region near the edge of the valve that is ornamented with a hyaline ring and a more defined mantle than the rapheless valve. Valvocopula may be closed, or complete, with internal projections of silica.
The genus contains both marine and freshwater taxa. Living cells have a solitary and adnate habit of growth. Cells possess a single plastid that is flat and C-shaped. Species of Cocconeis may be epiphytic on other algae, as well as on hard substrates (e.g. rock, sand). Cells grow with the raphe valve in contact with the substrate.