Eco-hydraulics traditionally aims at managing riverine systems in a semi-natural state while meeting human demands, assuming aquatic species are evolutionarily static. However, evidence of rapid evolution suggests that ignoring evolutionary dynamics of fish species might limit long-term effectiveness of eco-hydraulics frameworks. It remains unclear how freshwater fish adapt to human perturbation. Why are some fish populations more resilient to human perturbation than others? What are the genetic mechanisms behind it? To answer these questions, we genotyped eleven populations of three-spined stickleback in a regulated river system and collected data on river morphology, connectivity, flow regimes, physico-chemistry and parasite abundance through a combination of field surveys and modelling. Gene-environment association analysis detected strong signals of genetic divergence associated with hydraulic features. Gene ontology analysis revealed evolutionary responses that primarily involve functions in the nervous and sensory systems. These findings demonstrate that fish can evolve in response to river regulation, highlighting the need to transition from eco-hydraulics toward eco-evo-hydraulics. Our results can currently be accessed through a non-peer-reviewed bioRxiv preprint at Cai and Deflem et al. (2025), Fish Show Genetic Evolutionary Responses to River Regulation (DOI: 10.1101/2025.08.01.668107). This supporting dataset includes Genotyping-by-Sequencing data from 14 populations of three-spined stickleback collected in 2017 from the Demer Basin, Belgium, together with parasite and habitat data from the paired sampling sites. After quality filtering, 11 populations were retained and analyzed in Cai and Deflem et al. (2025).

FastQC, v0.11.9

Stacks, v2.54

BWA, v0.7.17

GATK, v4.2.0.0

VCFtools, v0.1.16

PLINK, v2.00a3.1