This study examined the nutrient budgets and biogeochemical dynamics in the coastal regions of northern Beibu Gulf (CNBG). Nutrient concentrations varied spatially and seasonally among the different bays. High nutrient levels were found in the regions with high riverine inputs and intensive mariculture. Using a three end-member mixing model, nutrient biogeochemistry within the ecosystem was estimated separately from complex physical mixing effects. Nutrient consumption dominated in most bays in summer, whereas nutrient regeneration dominated in winter, likely due to phytoplankton decomposition, vertical mixing and desorption. Through the Land-Ocean Interaction Coastal Zone (LOICZ) model, the robust nutrient budgets were constructed, indicating that the CNBG behaved as a sink of dissolved inorganic nitrogen, phosphorus and silicon. River-borne nutrient inputs were the dominant nutrient source, while residual flows and water exchange flows transported nutrient off the estuaries. This study could help us better understand nutrient cycles and nutrient sources/sinks in the CNBG.