Gomphoneis eriense var. variabilis is distinguished from other taxa considered within the basionym for this taxon. It differs from G. eriense var. angularis and G. eriense var. rostrata in that the valves are more rounded and have the broadest portion of the valve at the center. Gomphoneis eriense var. variabilis is distinguished from G. subherculeana by being narrower, and having finer striae. Gomphoneis eriense var. variabilis is distinguished from G. septa by smaller valves that are more broadly rounded.
This species has been confused with taxa in Gomphonema, specifically G. ventricosum and G. manubrium. Unlike those species, Gomphoneis eriense var. variabilis has longitudinal lines and striae composed of doubly-punctate striae.