<p>Low-inflow estuaries (LIEs) have unique biogeochemical cycles that favor nutrient accumulation, making these systems particularly vulnerable to cultural eutrophication. This study investigated a LIE (Baffin Bay, TX, USA) through high spatial resolution sampling of groundwater, porewater, and surface water. The concentrations and isotopic compositions of dissolved inorganic (δ¹⁵N-NH₄⁺, δ¹⁵N-NO₃⁻, δ¹⁸O-NO₃⁻) and organic (δ¹⁵N-DON) nitrogen were measured to investigate nitrogen sources and processing. Groundwater sampling sites were classified into three groups based on sample nutrient metrics and ancillary physical and chemical attributes. All groups exhibited high NO₃⁻ concentrations with distinct δ¹⁵N-NO₃⁻ to δ¹⁸O-NO₃⁻ correlations, implying different nitrogen processing. The NO₃⁻ stable isotope mixing model indicated differing source contributions from fertilizer, manure, and septic effluent among groups, underscoring the necessity of site-specific nutrient control plans. Porewater was dominated by NH₄⁺ that was likely contributed by remineralization and dissimilatory nitrate reduction to ammonium. Surface water, in contrast, exhibited a distinct nitrogen profile with high DON and low DIN concentrations. The DON stable isotope mixing model suggested allochthonous inputs dominated in the system, highlighting the crucial role of submarine groundwater discharge in delivering nutrients within LIEs and the need for nutrient control management in the bay and associated aquifers. The different nitrogen profiles of groundwater and surface water signify the importance of aquifer sampling in source investigation. This comprehensive nitrogen assessment and high-resolution sampling strategy should be applied to similar estuaries to fully understand nitrogen source infiltration, transformation, and processing across terrestrial and aquatic environments, aiding in the development of effective nutrient mitigation plans.</p>