Benthic and pelagic primary producers had their isotopic (ẟ13C, ẟ15N) and elemental (C, N) composition monitored in the Patos Lagoons estuary, in southern Brazil. The present dataset comprises temporal data obtained through seasonal samplings of C3 (Scirpus spp.) and C4 (Spartina densiflora) salt marsh plants, ephemerous bloom-forming drift macroalgae (Ulvophyceae), the widgeon grass Ruppia maritima, particulate (POM) and sedimentary (SOM) organic matter in shallow waters (< 2m) of a subtropical estuary from austral summer 2010 to autumn 2016. POM and SOM were collected as proxies of phytoplankton and microphytobenthos, respectively. Salt marsh plants were randomly sampled (N = 126) at a regularly flooded low marsh area, whereas submerged drift macroalgae (N = 29) and Ruppia plants (N = 14) were collected in adjacent mudflats. POM was collected (N = 33) by filtering water samples using glass fiber filter. SOM was obtained (N = 35) by removing superficial sediment. In laboratory, samples were processed and further analyzed for total organic carbon (TOC), total nitrogen (TN) and carbon (13C/12C) and nitrogen (15N/14N) stable isotopes ratios. With a total of 237 samples analyzed, this dataset provides key information on the isotopic and elemental composition of distinct estuarine primary producers and sources of particulate organic matter (POM and SOM) and their temporal variability in a highly variable aquatic environment. Such knowledge may add to ecological studies investigating food webs, biogeochemical cycles and sources tracking in coastal systems.
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