A comparison of results from mapping using a swath bathymetric sonar system in the Tay Estuary, Scotland, and remote sensing data on the position of frontal systems, indicates that the frontal systems are controlling the distribution of sedimentary features in the estuary. The boundaries between zones, defined by the advancing flood fronts and exiting fresh water, are sharply defined both by the front and the bottom bedforms. Static fronts, usually axial fronts, exist at well-defined bathymetric changes and result in relatively stable bedforms. However, measurements of current velocities at migrating fronts suggest that the vertical component of velocity accelerated at the front boundary will cause erosion at the bed and migrating bed features. Predictions of sediment movement and sediment feature migration rates across areas where these fronts migrate are confirmed by the bathymetric sidescan sonar results that show asymmetry of the sedimentary dune features. The use of new high-resolution sonar, together with its repeatable precision in locating sedimentary bedforms, has significant implications for long-term modelling of sediment transport in estuaries and other similar areas.