The hypothesis that contrasting hydrology induces divergent intraspecific phenotypic plastic responses in non-migratory freshwater fish was investigated. Morphologies of wetland and stream Galaxias gollumoides from South Island, New Zealand, at different stages of ontogeny, were examined. Phenotypic responses were tested for in a 2 × 2 factorial laboratory based controlled reciprocal transplant experiment with flow (current or no current) and source habitat (wetland or stream), as treatments. There was a shift in the overall head morphology of wetland current treatment G. gollumoides away from the wetland no current treatment, and toward the stream current treatment, demonstrating convergence in head morphology in the presence of flow of wetland and stream sourced captive G. gollumoides. Morphologies of captive reared G. gollumoides were also compared to developmental trajectories of morphological characters during the ontogeny of field reared first year, and adult conspecifics. In combination, experimental and field results support the hypothesis, finding habitat hydrology to be the potential mechanism inducing and maintaining intraspecific morphological divergence in G. gollumoides. Recognition of this mechanism inducing morphological divergence between populations also aids the taxonomic description of long genetically recognised lineages of co-members of the Galaxias vulgaris species complex.