Hydrological engineering alters habitat availability of cyprinid fish in semi-arid regulated river

Although Inter-Basin Water Transfer (IBWT) schemes have been implemented worldwide, their ecological impacts, especially on fish habitats, have received limited attention. This study evaluated the impact of flow regulation from an IBWT infrastructure on habitat suitability for two native cyprinid fish species ( Capoeta coadi and Chondrostoma regium ) in the Koohrang River in Iran. Field surveys were conducted across three seasons, covering 215 mesohabitats in two segments: an upstream control segment and a downstream impacted segment. Statistical comparisons showed that IBWT-induced flow regulation significantly altered hydrological conditions, reducing flow velocity, substrate size, depth, and canopy cover in the downstream segment. These changes resulted in a marked loss of habitat heterogeneity and simplification of mesohabitat structure downstream of the diversion dam and transfer tunnel. Mesohabitat composition was also different in the downstream segment, with a higher share of run habitats (45.3%) and fewer backwaters (6.2%) than in the upstream segment (31.5% runs and 15.4% backwaters). Fish habitat preferences differed across life stage for both species, with C. regium fingerlings preferring shallow, slower-flowing waters (<0.4 m/s) while C. coadi adults prefer deeper and faster-flowing habitats (0.5–2 m/s). For both species, the population composition differed significantly between river segments and was closely linked to the availability of key habitat characteristics, which also varied significantly between the segments (PERMANOVA: F = 7.41, p < 0.001) and among mesohabitat types (F = 8.75, p < 0.001). These findings indicated that large-scale water diversion has led to changes in habitat conditions that affected the populations of two native fish species.