Humans have altered river flows and lateral aquatic habitats. The expansion of agriculture in floodplains has resulted in landscapes dominated by irrigated farmland. A key challenge in water management is to conserve existing ecological communities and habitat heterogeneity, while simultaneously maintaining engineered infrastructure for agriculture. In this study, we focused on an artificial channel network for irrigation with a regulated flow regime and its function as habitat for various fish species. Differences of hydraulic conditions among channels and compositional changes in fish species were examined to clarify functional flow heterogeneity. Species turnover was analyzed using pairwise Simpson dissimilarity among sampling reaches. Species turnover was positively associated with Froude number (flow intensity) differences at intermediate discharges, and with differences in cross-sectional areas (flow magnitude) at low discharges. Drastic changes in inflows should be considered for the effective conservation of flow heterogeneity, even under a regulated flow regime. Improved engineering design to manage the hydraulic environment is one option for maintaining the ecological value of lateral waterbodies in human-dominated landscapes. Our findings provide insights into the importance of functional flow heterogeneity to conserve fish species diversity.