Previous investigations have documented spatial and temporal variations in the erosion threshold, erosion rate, and suspended sediment settling characteristics on an intertidal mudflat in a microtidal coastal plain estuary in the Danish Wadden Sea. The differences seem to be very much controlled by the effects of benthic biology rather than by physical parameters. In order to test to what extend biology may interact with the dynamics of fine-grained sediment in an entire estuarine system, these results have been transformed into four different sets of erodibility and settling characteristics which have been used as input to the 2D hydrodynamic numerical model MIKE 21 MT. The model was used to investigate the effect that differences in the benthic communities may have on the net deposition. The model included computation of hydrodynamics, wave fields and cohesive sediment dynamics. Based on the modelling results presented it is suggested that the benthic biological activity affects the net sedimentation pattern at the investigated site. The modelling results suggest that the presence of large numbers of the destabilising mudsnail Hydrobia ulvae results in higher net accumulation on the intertidal mudflat investigated. In contrast, biofilms may change net deposition by decreasing erosion, suspended sediment concentration and consequently the resulting settling flux of the suspended material. This study suggests that a numerical hydrodynamic model in combination with a fieldwork-based set-up of a cohesive sediment transport model may be used to describe and explain net sediment dynamics in a shallow coastal plain estuary. (c) 2006 Elsevier Ltd. All rights reserved.