Many estuaries worldwide are becoming more urbanised with heavier traffic in the waterways, requiring continuous channel deepening and larger ports, and increasing suspended sediment concentration (SSC). An example of a heavily impacted estuary where SSC levels are rising is the Ems Estuary, located between the Netherlands and Germany. In order to provide larger and larger ships access to three ports and a shipyard, the tidal channels in the Ems Estuary have been substantially deepened by dredging over the past decades. This has led to tidal amplification and hyper concentrated sediment conditions in the upstream tidal river. In the middle and outer reaches of the Ems Estuary, the tidal amplification is limited, and mechanisms responsible for increasing SSC are poorly understood. Most likely, channel and port deepening lead to larger SSC levels because of resulting enhanced siltation rates and therefore an increase in maintenance dredging. Additionally, channel deepening may increase up-estuary suspended sediment transport due to enhanced salinity-induced estuarine circulation.The effect of channel deepening and port construction on SSC levels is investigated using a numerical model of suspended sediment transport forced by tides, waves and salinity. The model satisfactorily reproduces observed water levels, velocity, sediment concentration and port deposition in the estuary, and therefore is subsequently applied to test the impact of channel deepening, historical dredging strategy and port construction on SSCs in the Estuary. These model scenarios suggest that: (1) channel deepening appears to be a main factor for enhancing the transport of sediments up-estuary, due to increased salinity-driven estuarine circulation; (2) sediment extraction strategies from the ports have a large impact on estuarine SSC; and (3) maintenance dredging and disposal influences the spatial distribution of SSC but has a limited effect on average SSC levels.