Nutrient (phosphorus and nitrogen) concentrations in aquatic ecosystems (estuaries, lakes, wetlands, and rivers) are influenced by loadings from watershed, tributaries, and atmospheric deposition; transport and mixing by hydrodynamic processes (circulation, wave, and turbulent mixing); and various transformation processes (desorption, adsorption, and mineralization, etc.). In deep temperate aquatic ecosystems, vertical density stratification can significantly influence the distribution of dissolved oxygen that can, in turn, affect the nutrient dynamics in the ecosystem. In shallow subtropical and tropical aquatic ecosystems, hydrodynamic processes often lead to significant exchange of sediments and nutrients between the water and sediment columns. This chapter reviews a few recent studies in subtropical aquatic ecosystems to demonstrate the significant effects of hydrodynamic processes on nutrient distribution. In addition, the chapter provides a brief review of models for simulating nutrient distribution in estuaries and lakes. Deficiencies of regression-based models and box-type models necessitate further development of multidimensional process-based models for assessing the impact of nutrient loading on water quality in aquatic ecosystems.