<p>Increasing concerns regarding aquatic ecological health and eutrophication driven by urbanization and human activities have highlighted the need to understand primary productivity (PP) dynamics in aquatic ecosystems. This study investigated the spatial distribution of PP across the Weihe River Basin, China using inverse distance weighting and analyzed the influence of different land uses and water physical-chemical parameters on PP using Mantel test and Spearman analysis. Significantly spatial heterogeneity in PP concentrations, ranging from 0.458 to 3262.807 mg C/(m²·d), was observed with high-PP sites clustered in the middle-lower reaches dominated by farmland-construction land mosaics. Core drivers included light availability (Secchi depth and sunlight duration) and phytoplankton biomass (chlorophyll-<i>a</i> (Chl-<i>a</i>)), while water temperature exhibited threshold-dependent effects. Total organic carbon played dual roles, promoting PP concentrations in low-Chl-<i>a</i> regions, but suppressing it under high-Chl-<i>a</i> regions. Dual-scale buffer analysis (500 and 1000 m buffer zones) revealed PP heterogeneity stemed from interactive land use configurations, rather than isolated types. Balanced construction land-to-farmland ratio (0.467–2.890) elevated PP concentrations in human-dominated basins (the main stem of the Weihe River and Jinghe River), whereas excessive agricultural homogenization reduced PP likely due to fertilizer saturation and algal self-shading. Ecologically sensitive basins (the Beiluohe River Basin) demonstrated distinct patterns, in which PP concentration was regulated through natural-agricultural synergies. These results deepened the understanding of land use effects on aquatic PP, providing a theoretical basis for optimizing land use strategies to reconcile eutrophication control with ecological productivity in human-stressed basins.</p>