Integrated dissolved inorganic nutrient fluxes (nitrite, nitrate, ammonium, phosphate and silicate) between Patos Lagoon estuary (PLE), Brazil, and the inner continental shelf of the southwest Atlantic Ocean, were estimated from averaged water column nutrient concentrations and water fluxes (method 1 – M1). Daily surveys were carried out for 30 days, spanning from Feb-22 to Mar-23 of 2021 during late austral summer drought, at two stations — one next to the estuary mouth, the other in the inner estuary, at the interface between the estuary main channel and a shallow embayment called the Arraial bight. On average, PLE delivered dissolved inorganic phosphorus (DIP), nitrogen (DIN) and silicate outfluxes to the adjacent continental shelf at rates of 22.4 ± 596.1, 89.8 ± 207.3 and 1715.9 ± 3283.2 × 103 mmol m−2 d−1, respectively. Budgets for DIP and DIN were computed by the LOICZ box model approach (method 2 – M2) considering Patos Lagoon divided into its limnic (fresh, mean salinity 2 psu) and estuarine (brackish, mean salinity 18.5 psu) regions. The residual fluxes for DIP and DIN from PLE to the inner continental shelf were similar to those of M1, but the complete budget (M2) revealed that PLE also imported DIP, at a positive exchange rate between PLE and coastal waters. There is evidence that DIP is supplied by Plata Plume Water. Net ecosystem metabolism (NEM) and N-fixation – denitrification were assessed through the LOICZ budgets for DIP and DIN, respectively. Denitrification prevailed in both limnic and estuarine regions. Estimated NEM indicated weak autotrophy in the limnic region, and net heterotrophy in the estuarine region. The net heterotrophy in the estuarine region was mainly attributed to nitrogen limitation due to low allochthonous supply by river discharge, and N-loss by denitrification during austral summer drought conditions.