The physical regime of Limfjorden in northern Denmark has been investigated with the aim of defining its role in controlling the food supply to a community of benthic filter feeders, which is dominated by commercially valuable mussels. A two-week campaign of hydrodynamic observations at different spatial scales was undertaken in May/June 2003 as part of an interdisciplinary study. The results reveal that the water column in Limfjorden switches periodically between stratified and mixed conditions in response to meteorological forcing. During calm periods, stratification develops in response to solar heating. This stratifying tendency is opposed principally by wind stirring indirectly through wave motions. Due to the low velocities, there is very little generation of turbulence due to shear stresses at the bed. The mussels appear to have a subtle effect on turbulence levels very close to the bed, but in this system the effect of mussels on the hydrodynamics of the whole water column is limited. A reduced physics model of the competition between these processes has been developed, which incorporates the effects of waves and of shallow water on the absorption of solar radiation. When forced by observed data for wave activity and surface heating, the model simulates the principal features of the observed evolution of water column stability. Stratification is usually detrimental to mussel growth, as it limits access of mussels to food in the upper water layers. However, if mussels are capable of depleting the whole water column under fully mixed conditions, brief periods of stratification could theoretically act as a temporary refuge for phytoplankton, allowing the population to recover. The ultimate effect of this hydrodynamic switching of the system needs further assessment. (c) 2005 Elsevier B.V. All rights reserved