Abstract: River-estuary is an important component of earth system linking land and ocean cycling of materials. Human activities and climatic change have substantially altered nutrient cycling accompanied by series of negative ecological effects (e.g., eutrophication, harmful algal bloom, hypoxia, acidification). Based on the recent studies using in-situ observation, experimental and modeling approaches as tools, this paper summarized current understanding of the subtropical Jiulong River-Estuary system in Southeast China, including long-term change in nutrients (nitrogen, phosphorus, silica) in terms of concentration and flux and controlling factors, aquatic denitrification, nutrient retention by cascade dam reservoirs, and impacts of climate change (storm events and warming) on nutrient delivery and cycling. Potential effects of nutrient variation on aquatic ecosystems are also discussed. Current results suggest that small and medium-sized rivers are more sensitive than large rivers to human and climate perturbation in terms of nutrient biogeochemistry and ecology. Research priorities on nutrient biogeochemistry of the watershed-estuary-coast continuum under global change were proposed: (1) Capture nutrient changes at various temporal and spatial scales through intensive field observation and reveal key processes and drivers of nutrient cycling using multidisciplinary integrated study approach. (2) Evaluate the uniqueness of small and medium-sized rivers and their role in regulating global or regional climate and environment. (3) Further study the nutrient retention by river dams and coastal wetlands and associated effects on the aquatic ecosystems.