Coastal morphodynamic and hydrodynamic processes impose a first-order control on biogeochemical cycling and distribution of benthic habitats. However, little is known on how biota in turn affect sediment transport, biogeochemical cycling and morphodynamics at a regional scale and long-term. Here we firstly present a mini-review of recent progress on numerical modeling of interactions between benthic biota, biogeochemical cycling and coastal morphodynamics. Special focus is laid on 1) the synergetic effects of dominant benthic functional groups on sedimentation process, and 2) the macrobenthic response to changing morphological, hydrodynamic and biogeochemical conditions. In a second part we present preliminary results from a case study area (Jade Bay, Wadden Sea) based on simulations using a coupled hydrodynamic-biogeochemical-morphodynamic model and comparison with biogeochemical and taxonomic field monitoring data. The aim is to understand benthic ecosystem functioning and to identify the main drivers of coastal ecosystem changes for better prediction of their future development.