The lightly silicified valves of Skeletonema often collapse when dried and dissolve with standard processing methods. The tubular processes around the top of the mantle link frustules into long colonies. A marginal fultoportula lies at the base of each tubular process. Occasionally, valves produce a ring of flattened processes instead of the tubular processes. Each flattened process has a rimoportula.
Skeletonema grows primarily in marine and estuarine habitats. Species within the genus are known to form large blooms in eutrophic and saline inland lakes and large rivers. Specimens of Skeletonema are often overlooked.