Abstract High-dam reservoirs can significantly affect nutrient cycling processes across the globe. However, the research community now has two contradictive views (i.e., retention versus transformation) about the impact of high-dam reservoirs on nutrient cycling due to incomplete information obtained from limited field samplings. To resolve this issue, we develop a physically-based, three-dimensional water quality model to examine the spatiotemporal distributions of biogenic elements (nitrogen and phosphorus) in high-dam reservoirs with high spatial and temporal details. We apply the model to the Xiaowan Reservoir, a representative high-dam reservoir in the Lancang River Basin. By scrutinizing the spatiotemporal distributions of biogenic elements across space and over time, we find a unique “retention-transformation-transportation” process of nitrogen and phosphorus in the high-dam reservoir, with dominant transformation occurring in the water zone before the dam during non-flood period while dominant retention occurring in the middle part of a reservoir during flood period. We further find that transformations of biogenic elements are enhanced only in low-temperature and low-oxygen environments. Our findings show solid scientific basis to resolve the contradictive views about nutrient cycling mechanisms in high-dam reservoirs, and provide important policy implications for the operation of high-dam reservoirs to achieve improved water quality while maintaining clean energy supply.