Pinnularia nodosa is distinguished from other Pinnularia species with triundulate margins by the mottled pattern in the axial and central areas.
Valves of Pinnularia nodosa var. percapitata are more markedly triundulate, with more distinctly capitate apices. The central undulation of the variety is usually a bit wider than the distal undulations and valves are wider (7.7-10.6 µm).