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The spatial analysis of biota, particulate organic matter, and sediments for stable isotopes of carbon (δ13C), nitrogen (δ15N), and sulfur (δ34S) have proved useful for identifying patterns in productivity, nutrient pollution, and relationships between biological and physiochemical variables at the local and global scales. Yet such approaches are rarely applied to studies of lagoon or estuarine metabolism. Focusing on Bahía San Quintín, a heterotrophic seagrass-dominated lagoon on the Pacific coast of Baja California, México, we report on spatial patterns in surficial sediment CNS stable isotopic ratios as tracers of lagoon biogeochemical function. Stable nitrogen isotopes highlighted potential spatial variability in the balance between denitrification and nitrogen-fixation within the lagoon and identified an association between elevated δ15N levels and oyster culture, suggesting that oyster presence may be enhancing N2 production. Spatial patterns in δ34S covaried with sediment particle size, underlining the importance of sediment texture in determining the depth of sub-oxic-anoxic redox zones. Sediment carbon stable isotope ratios highlighted the lack of incorporation of seagrass carbon into seagrass meadow sediments, thus emphasizing the importance of phytoplankton or microphytobenthos for carbon accumulation in seagrass meadows. This report highlights the value of sediment isotopic values in corroborating spatial patterns in estuarine metabolism or macronutrient processing identified from chamber or flux-based studies. Stable isotope mapping can provide a useful addition to assessment of estuarine metabolism, or act as a stand-alone tool for generating hypotheses, identifying the influence of spatial gradients, and/or suggesting prime locations for investigation of microbial abundance or function. [ABSTRACT FROM AUTHOR]