The estuary of the Perequê River has small dimensions, being the main fluvial input in the Porto Belo Bight and has never been investigated regarding its oceanographic features. A field campaign was carried out where physical and chemical variables were recorded in a fixed sampling station during a complete tide cycle: water level, currents, salinity, temperature, turbity, pH, dissolved oxygen (DO), dissolved inorganic nutrients (ammonium - NH4+, nitrite - NO2-, nitrate - NO3-, silicate - Si, and phosphate - PO43-) and chlorophyll-α. A longitudinal survey was done along the estuary to evaluate the salt intrusion. Results showed that flood tide currents were stronger than the ebb currents, with values of 0,5 and -0,21 m.s-1, respectively. The salinity ranged between 17 and 29, with small stratification during the low tide and no stratification during the high tide. The time variation of the salinity presented a well defined front system, where the salinity presented low values during the low tide and a steep increase during the flood, where the water becomes with coastal water characteristics. The concentration of dissolved inorganic nitrogen (DIN) reached very high levels, reaching 97,7 µmol.L-1, mainly because the contribution of NH4+ (74%), indicating presence of domestic sewage. The DIN presented inverse relationship with salinity, meanwhile the chlorophyll showed direct relationship. The silicate and phosphate did not presented relationship with salinity. The water quality in the lower estuary was mainly driven by estuary-shelf exchanges, and presented poor horizontal mixing between estuarine and coastal waters.