We use data from Geosat altimeter and from 10 inverted echo sounder (IES) moorings deployed in the SW Atlantic Ocean off the Argentine continental shelf to investigate several aspects of the dynamics of the upper layer in the Brazil-Malvinas Confluence region. We use the altimeter data to estimate the sea height anomalies at each IES location and use the IES data to compute the upper layer thickness, taken in this work to go to the depth of the 8°C isotherm. We first discuss the sea height and upper layer thickness variations caused by the passage of the Brazil Current, Malvinas Current, and warm anticyclonic and cold cyclonic eddies. We introduce a two-layer model in which we decompose the sea height into its baroclinic and barotropic contributions. We then propose a method to monitor the thickness of the upper layer and the barotropic and baroclinic transports as a function of the sea height anomalies and the statistics of the upper layer thickness and reduced gravity for the region. We compute the reduced gravity values from the slope of a linear fit between the sea height anomalies and the upper layer thicknesses. We estimate the reduced gravity values for this region to range from 0.005 to 0.011 m s−2. We also estimate the mean barotropic sea height difference using two methods: conservation of mass and conservation of potential vorticity. Finally, we compute the time series for the baroclinic and barotropic transports during the Geosat Exact Repeal Mission time period. Our results suggest that the mean baroclinic transport in the upper layer decreases from 12 Sv at around 35°S to 7 Sv at 37°S. Our results also indicate that there is a significant barotropic contribution to the upper layer transport in the confluence region.