We investigated associations of fish assemblages and habitat characteristics (e.g., morphology and water chemistry) from 45 natural lakes and reservoirs in Iowa to determine whether species or trophic guild composition and environmental correlations were concordant between waterbodies of different origins. Overall, fish assemblage composition between natural lakes and reservoirs was consistently dissimilar based on a permutational multivariate ANOVA. Species composition from nonmetric multidimensional scaling ordinations for reservoirs was correlated with a variety of limnological and physical characteristics, whereas species composition and trophic composition of natural lakes were weakly associated with habitat characteristics. Species richness was positively related to waterbody and watershed size for reservoirs but not for natural lakes. Conversely, species richness was negatively correlated with increasing eutrophic conditions in natural lakes but not in reservoirs. Overall, distinct differences in assemblage composition were observed between natural and artificial lentic ecosystems and may have resulted from underlying differences in limnological, physical, and anthropogenic influences between systems. Dissimilar management legacies between waterbody types, such as limited or no stocking of nonrecreationally important species and the use of piscicides, may have additionally had overriding effects on the observed assemblage–environmental relationships. For instance, lower trophic richness and species richness in reservoirs appeared to have resulted from replacement of a diversity of small-bodied native species by relatively few commonly stocked sport fishes. Our results emphasize the need to consider waterbody origin and the potential influence of historical or current management strategies on fish assemblage characterization and subsequent inferences made from environmental correlations.