This thesis investigates the origins of large sedimentation volumes in the Port of Santos, São Paulo - Brazil. The port is located in the Santos - São Vicente estuarine system, delimited by scarps and subject to intense rainfall. The terminals are placed inside the estuary and their access is provided by a 24 km long channel with mean depths of 15 m DHN, subject to annual maintenance dredging with volumes in the order of 4 Mm³ [CODESP, 2016a]. A literature-based sediment mass balance is formulated for the system. Sediment sources and sinks are assessed based on data of the period 2005 to 2012 and expert judgment. The largest sediment input is given by winter storms (65%) followed by river sediment loads (25%). Up-estuary import of fine sediment is found as a third source, computed from the deficit between sources and sinks (trapping in the mudflats and maintenance dredging). An explorative process based model is set to evaluate the hypothetical sediment balance and expand the understanding of the system behavior. A period of six months is simulated to capture the expected seasonal variability in salinity gradients. Conditions for fluid mud formation are found in the entire channel. A rerun with salinity switched off promotes an expressive reduction (70%) in the cumulative fine sediment import. Up-estuary sediment transport is found as a result of salinity-induced residual currents, which increase in strength with deeper channels [van Maren et al., 2015]. Fine sediment deposits in the final stretches of the channel that probably have been accounted in previous studies as from river discharges, according to this study are provided from marine sources. Model results suggest an annual import of 1.1 Mton of sediment, six times larger than the literature-based estimate. Additionally, results indicate that little quantity of riverine sediment reaches the channel. The literature mass-balance is therefore modified to incorporate these findings: river contribution is set to 15%, up-estuary transport to 30%, and winter storms to 55%.