Nitrogen (N) availability strongly regulates estuarine primary productivity, yet the mechanisms linking multiple N-source utilization with carbon-nitrogen (C-N) coupling remain insufficiently understood. Although Redfield stoichiometry predicts a broad balance between C-based primary productivity (PP_C) and N-based primary productivity (PP_N), field observations often show marked PP_C-PP_N decoupling, particularly in eutrophic estuaries where phytoplankton communities and N forms vary sharply along environmental gradients. Here, we investigated summer surface waters of the Pearl River Estuary using combined ¹³C-¹⁵N isotope tracer incubations. Uptake rates of C and four N forms, including ammonium (NH₄⁺), nitrate (NO₃^-), nitrite (NO₂^-), and urea, were quantified to evaluate their contributions to PP_N and their relationships with PP_C. Phytoplankton community composition was also examined to assess ecological controls on N-source utilization. The phytoplankton community showed clear spatial variability. Diatoms dominated the upper and lower estuary, whereas Synechococcus prevailed in the outer estuary. N uptake was dominated by reduced N, with NH₄⁺ contributing the largest proportion followed by NO₃^-, urea, and NO₂^-. The important contribution of urea indicates that organic N can substantially support phytoplankton N demand in the Pearl River Estuary. NO₃^- uptake was mainly associated with phytoplankton biomass, especially diatoms, whereas NH₄⁺ and urea uptake were mainly regulated by substrate variability. PP_N estimated from N uptake exceeded PP_C, indicating a clear imbalance between C and N assimilation. This decoupling was mainly associated with differences in N-source utilization and phytoplankton community composition. Size-fractionated results further suggested that smaller phytoplankton, especially picophytoplankton, may enhance the role of urea in sustaining productivity in offshore waters. These findings indicate that N-source preference and phytoplankton size structure jointly regulate PP_C-PP_N balance, providing a mechanistic basis for better evaluating C-N coupling, productivity dynamics, and biogeochemical responses to changing nutrient inputs in subtropical estuaries.