The objective of this study was to test if morphological differences in pumpkinseed Lepomis gibbosus found in their native range (eastern North America) that are linked to feeding regime, competition with other species, hydrodynamic forces and habitat were also found among stream- and lake- or reservoir-dwelling fish in Iberian systems. The species has been introduced into these systems, expanding its range, and is presumably well adapted to freshwater Iberian Peninsula ecosystems. The results show a consistent pattern for size of lateral fins, with L. gibbosus that inhabit streams in the Iberian Peninsula having longer lateral fins than those inhabiting reservoirs or lakes. Differences in fin placement, body depth and caudal peduncle dimensions do not differentiate populations of L. gibbosus from lentic and lotic water bodies and, therefore, are not consistent with functional expectations. Lepomis gibbosus from lotic and lentic habitats also do not show a consistent pattern of internal morphological differentiation, probably due to the lack of lotic–lentic differences in prey type. Overall, the univariate and multivariate analyses show that most of the external and internal morphological characters that vary among populations do not differentiate lotic from lentic Iberian populations. The lack of expected differences may be a consequence of the high seasonal flow variation in Mediterranean streams, and the resultant low- or no-flow conditions during periods of summer drought.