In the upper Paraguay River basin, which includes the Pantanal, one of the largest wetlands in the world, rivers connection the surrounding upland plateaus with lowland floodplains. Agriculture, erosion, urban effluent, and hydropower in the uplands can alter the transport of materials by rivers to the Pantanal. Information about material transport, particularly nutrients, is still insufficient to evaluate changes. In this study we estimated rates of dissolved and suspended material transport from the upland watersheds into the Pantanal, and through the Paraguay River, and calculated mass balances of these flows to reveal net losses and gains inside the Pantanal. We sampled fifteen tributaries and the Paraguay River for seven years. The annual water balance in the basin was almost complete, with a deficit of only 11%. Predicted:Observed ratios close to one indicated a near balance between inputs and outputs for dissolved solutes and nutrients, however sedimentation losses of suspended solids and particulate carbon were significant. In spite of a high degree of river-floodplain contact, no significant changes on solutes concentrations were observed between inputs and outputs, enough to alter the transport of solutes though the Pantanal, indicating equilibrium in biogeochemical process on floodplain.