Valves of Brachysira are linear to linear-lanceolate in outline. The ends of the valves, or apices, may be rounded to protracted. In general, the valves are symmetric to the apical axis, although some specimens may have a slight, to strong, asymmetry to the transapical axis. The striae are finely punctate, and form longitudinal undulations. The raphe is straight and the axial area is narrow. In the SEM, an elevated siliceous ridge separating the valve face and mantle on the external valve surface is visible. Cells possess a single plastid.
Brachysira may grow singly and unattached, or it may grow at the ends of mucilaginous stalks. Species within the genus are broadly distributed across North America in a range of trophic states, with individual species characteristic of oligotrophic to dystrophic waters. Cell abundance may be especially high in low conductivity and low pH waters, for example, in bog habitats. The genus is primarily benthic, but may also be found in lake plankton, where cells may become entrained.