Tidal sand waves are dynamic bedforms found in coastal shelf seas. Moreover, these areas are inhabited by numerous benthic species, of which the spatial distribution is linked to the morphological structure of sand waves. Especially the tube‐building worm Lanice conchilega is of interest as this organism forms small mounds on the seabed which provide shelter to other organisms. We investigate how the interactions between small‐scale mounds (height ~dm) and large‐scale sand waves (height~m) shape the bed of the marine environment. To this end, we present a two‐way coupled process‐based model of sand waves and tube‐building worm patches in Delft3D. The population density evolves according to a general law of logistic growth, with the bed shear stress controlling the carrying capacity. Worm patches are randomly seeded and the tubes are mimicked by small cylinders which influence flow and turbulence, thereby altering sediment dynamics. Model results relate the patches with the highest worm densities to the sand wave troughs, which qualitatively agrees with field observations. Furthermore, the L. conchilega tubes trigger the formation of sandy mounds on the seabed. Due to the population density distribution, the mounds in the troughs can be several centimetres higher than on the crests. Regarding sand wave morphology, the combination of patches and mounds are found to shorten the time‐to‐equilibrium. Also, if the initial bed comprised small sinusoidal sand waves, the equilibrium wave height decreased with a few decimetres compared to the situation without worm patches. As the time scale of mound formation (years) is shorter than that of sand wave evolution (decades), the mounds induce (and accelerate) sand wave growth on a similar spatial scale as the mounds. Initially this leads to shorter sand waves than they would be in an abiotic environment. However, near equilibrium the wavelengths tend towards their abiotic counterparts again.