Abstract Human activities have widely disrupted the spatial ecological processes critical for population and ecosystem integrity. Local effects of altered sediment regimes in rivers are well explored, but how they impact connectivity at a catchment scale is less explored. In this paper we document evidence for altered metapopulation dynamics for a headwater specialist, blackspotted topminnow (Fundulus olivaceus) in catchments with geomorphically dynamic river mainstems. We quantified decade‐scale patterns of fluvial geomorphic activity via planform analysis of historical and recent aerial imagery, and patterns of gene flow in F. olivaceus via analysis of single nucleotide polymorphisms, identified by genotype‐by‐sequencing. Mainstem streams narrowed and increased in sinuosity, probably in recovery from historic flood events. Substantial variability in response indicated underlying differences due to differential disturbance history and catchment sensitivity to change. Multiple analytical approaches all found geography to be a major factor in genetic structuring among catchments. Metrics of genetic differentiation and heterozygosity for F. olivaceus within catchments were related to the degree of geomorphic change inferred from a multivariate composite metric. Catchments with more geomorphic change tended to have more population structuring. Five populations assigned to adjacent catchments. Analysis of heterozygosity in presumed donor, recipient, and mis‐assigned catchments indicated founder effects in recipient catchments and probable subsequent allopatric recolonisation following local extirpations. Our results demonstrate complex nonlocal effects of channel evolution on metapopulation dynamics in a pool‐dwelling non‐lithophilous headwater specialist. Our integrative approach allows strong insight into deeper effects of geomorphic processes on aquatic ecosystems. F. olivaceus is ecologically dissimilar to taxa traditionally anticipated to respond to sediment‐related disturbances and demonstrates how broader channel morphological change can affect habitats beyond sedimentation of the stream bed.