The distinctly punctate striae are characteristic of this species and differentiate it from N. alpina. Nitzschia amphibia is often found in the same habitats as N. amphibioides and is of similar size and shape. However, N. amphibia lacks the thickened fibulae that are characteristic of N. amphibioides. Furthermore, N. amphibia has a prominent central nodule, which N. amphibioides lacks.