Abstract The susceptibility of coastal environments to shifts in the biogeochemical cycles of carbon and nutrients driven by anthropogenic pressure and climate change is a real challenge for the scientific community. This paper evaluated the effects of an extreme rainfall event over the nutrients and carbonate parameters in two polluted tropical estuaries. Surface water samples were taken seasonally along a salinity gradient in the Capibaribe and Barra de Jangadas estuaries in order to investigate the spatial and seasonal variability of dissolved nutrients, chlorophyll-a, dissolved oxygen, total alkalinity, inorganic carbon, partial pressure of CO2 (pCO2) and CO2 fluxes. The increased riverine influence caused by the fluvial flooding during the extremely rainy season augmented the nitrogen concentrations in the plumes, which also presented reduced salinity, alkalinity and dissolved oxygen values. In the Capibaribe plume it has also shifted the mean CO2 flux value of - 4.01 mmolC m-2 d-1 during the dry season, to a positive mean flux of + 5.7 mmolC m-2 d-1 during the rainy season. Within the estuaries the BOD5,20 and dissolved phosphorus values were higher during the dry season (p<0.0001), they showed positive correlation with the phytoplanktonic blooms that reached a chl-a value of 85 mg m-3 in the Capibaribe. The high alkalinity found in both estuaries, with mean values between dry and wet seasons respectively from 1808 to 1373 µmol kg-1 in the Capibaribe estuary and 1616 to 1058 µmol kg-1 in Barra de Jangadas estuary, may act as a buffer to the process of coastal acidification due to eutrophication. The increased rivers discharge lead to a greater transport of organic matter and nutrients to the coast, decreasing the oxygen availability and shifting the metabolic status of the estuarine plume to heterotrophic, whereas increased the water quality within the estuaries due the flushing promoted by the extreme rainfall event.