The net growth rate of marine zooplankton entering the Westerschelde estuary was investigated using an advective-dispersive transport model that simulates zooplankton biomass behaving conservatively in the estuary. Total biomass of marine zooplankters in the Westerschelde was much lower than what would be expected based on transport alone, indicating negative growth rates in the estuary. Including a net consumption term in the transport model allowed the estimation of total net mortality. About 3% of all marine zooplankters that enter the Westerschelde with the flood currents are retained in the estuary, where they die. On average, 5% of the total marine zooplankton biomass in the estuary died per day. Each year a net amount of about 1500 t of zooplankton dry weight (DW) is imported from the sea to the estuary. Thus in the Westerschelde the marine zooplankton persists mainly due to continuous replenishment from the sea. Average net production/biomass rates of the major marine zooplankton species varied from -0.02 g DW (gDW) -1 d -1 ( Temora longicornis ) to -0.39 g DW (gDW) -1 d -1 ( Pseudocalanus elongatus ). In the estuary, the differential mortality of these species resulted in shifts in dominance within the zooplankton community relative to that in the sea. Possible causes of this zooplankton mortality are discussed.