Understanding material input changes within estuarine environments is essential to assess nutrient exportation to nearshore coastal waters and their influence on coastal and oceanic region ecology. This study is aimed at describing the nutrient and phytoplanktonic biomass dynamics in a tropical estuary, affected by sewage and agricultural run-off, through a microcosm experiment. Dissolved organic and inorganic N (DON and DIN), and P (DOP and DIP), chlorophyll-a and silicate were measured during dry and rainy periods to compare the inner and outer portions of the Cachoeira River estuary. In the inner portion at the beginning of the experiment, NH3 + NH4 + , DOP, SiO4 -4 and PO4 3 concentrations were highest during the rainy period, while, the highest values of chlorophyll-a and DON occurred in the dry period. The nutrient assimilation by phytoplankton was responsible for N-ammoniacal, nitrate and phosphate decrease. Nitrate was the greatest source of nitrogen and was totally depleted into the incubation days. Nitrification occurred, but possibly was not the most relevant mechanism in removal of NH3 + NH4 + . DON and DOP were probably used by phytoplankton. The highest nutrients concentrations in the inner portion confirmed the influence of sewage discharge nutrient dynamics and a water renewal in the outer portion indicated by previous studies in the Cachoeira River estuary.