Valves are asymmetric to the apical axis. Like Nitzschia, the raphe is contained within a canal and eccentrically positioned on the valve margin. In Hantzschia, the raphe is always located on the concave, or ventral, margin of the valve. Striae are uniseriate.
The genus Hantzschia differs from Nitzschia in symmetry. Within a Hantzschia frustule, the raphes of the two valves are on the margin of the same side. In contrast, within a Nitzschia frustule, the raphes of the two valves are on opposite margins. This arrangement of the raphe is termed "hantzschiod symmetry" and "nitzschiod symmetry", respectively. Hantzschioid or nitzschioid symmetry of a frustule is the result of the position of nucleus at cell division (Pickett-Heaps et al. 1980).
Hantzschia has a greater number of species in marine habitats than in freshwaters. It is characteristic of temporary aquatic habitats and, in particular, the genus is often indicative of soil habitats.