We use a linear stability approach to develop a process-based morphodynamic model including a two-way coupling between tidal sand wave dynamics and benthic organisms. With this model we are able to study both the effect of benthic organisms on the hydro- and sediment dynamics, and the effect of spatial and temporal environmental variations on the distribution of these organisms. Specifically, we include two coupling processes: the effect of the biomass of the organisms on the bottom slip parameter, and the effect of shear stress variations on the biological carrying capacity. We discuss the differences and similarities between the methodology used in this work and that from ‘traditional’ (morphodynamics only) stability modelling studies. Here, we end up with a 2×2 linear eigenvalue problem, which leads to two distinct eigenmodes for each topographic wave number. These eigenmodes control the growth and migration properties of both sand waves and benthic organisms (biomass). Apart from hydrodynamic forcing, the biomass also grows autonomously, which results in a changing fastest growing mode (FGM, i.e. the preferred wavelength) over time. As a result, in contrast to ‘traditional’ stability modelling studies, the FGM for a certain model outcome does not necessarily have to be dominant in the field. Therefore, we also analysed the temporal evolution of an initial bed hump (without perturbing biomass) and of an initial biomass hump (without perturbing topography). It turns out that these local disturbances may trigger the combined growth of sand waves and spatially varying biomass patterns. Moreover, the results reveal that the autonomous benthic growth significantly influences the growth rate of sand waves. Finally, we show that biomass maxima tend to concentrate in the region around the trough and lee side slope of sand waves, which corresponds to observations in the field.