Interpretation of fossil assemblages in mixed energy environments, such as estuaries, is complex due to the accumulation of material from different sources. In such environments, different proxies may result in contrasting interpretations, as is illustrated by the case of the Scheldt estuary in northern Belgium: during a phase of increased landward tidal ingression between 7000 and 5000 cal BP, mud was deposited, including microfossils that indicate increased salinity, while macrofossil records from the same deposits indicate tidal freshwater environments. By combining multiple proxies, sedimentological analysis and multivariate statistics, it is concluded that considerable landward sediment transport by tidal pumping, possibly enhanced by storms, explains how marine and brackish microfossils are massively present in freshwater tidal deposits. We propose an approach that combines the easily transported microfossils with the more local macrofossils to obtain a coherent reconstruction of the local estuarine environment, and to better understand the sedimentological processes in the wider region.