This dataset was acquired in a research program funded by the European Commission known as ECOSUD (Estuaries and Coastal Areas: Basis and Tools for a more Sustainable Development). It includes the realization of 4 field campaigns (one every season), where morphologic, meteorological, hydrodynamic, hydrographic, and water quality data were acquired. Sampling campaigns were performed under several salinity conditions in the estuary. The first 2 cruises were conducted in Mangueira Bay and the southern estuarine portion of Patos Lagoon (Rio Grande Channel) in order to obtain contrasting data. Samples were taken in October 2002 (austral spring) and June 2003 (austral winter). 2 additional cruises were then conducted in the remaining seasons: one in December 2003 (austral summer) and the other in April 2004 (austral fall). At each sampling station, the water column was sampled at the surface using a Van Dorn-like bottle. Samples were stored in polyethylene bottles and kept at 5°C until they arrived at the laboratory, where they were either promptly analyzed or preserved. SPM samples were analyzed using the methods described by Baumgarten et al. (Baumgarten, M., Rocha, J., and Niencheski, L.: Manual de Análises em Oceanografia Química, FURG, Rio Grande, Brazil, 1996).