Combining observations with numerical simulations of hydrological and biogeochemical processes, this thesis investigates how land surface characteristics, human activities, atmospheric processes, and climate change influence the spatiotemporal distributions of water and nutrient fluxes in the Pearl River Basin and the urbanized Pearl River Delta (PRD) downstream. We show that land use and soil texture affect water redistribution within soil profile and determine active water flux zones. Spatially, surface flow, lateral flow, actual evapotranspiration, and aquifer flow are active in urban areas, forests, agricultural regions, and coarse-textured soils, respectively. Streamflow increases are more pronounced in the eastern part of the basin than in the western part. Temporally, streamflow exhibits nonlinear changes, with a slight reduction in the near-term followed by a significant increase in the long-term under climate change. These spatiotemporal hydrological patterns are attributed to the combined effects of summer monsoon variability and land surface processes. Subsequently, we link these hydrological processes with nutrient fluxes, identifying that the coupling of transport mediators and nutrient sources jointly regulates nutrient species from non-point sources (NPS). Agricultural lands, forested areas, and pastures in the basin contribute nutrient fluxes through fertilizers with flows and sediment, soil nitrate levels with lateral flow, and soil-derived labile phosphorus with surface flow, respectively. In the PRD, point sources dominate nutrient contributions, primarily driven by domestic wastewater. Meanwhile, NPS in the urban areas is controlled by soil sources, and these areas exhibit the highest transport efficiency of pollution due to elevated surface flow and sediment yield. Together, these factors result in a weakened core-periphery pollution structure in the PRD. Overall, this thesis provides holistic scientific insights for managing water resources and water quality in socioeconomically active southern China, as well as in other terrestrial systems worldwide.