Tidal basins and estuaries are typified by strong environment gradients that drive sedimentation processes on multiple spatial scales. At the scale of tidal basins and estuaries, flow and current dynamics drive gradients of increasing mud concentrations from the tidal inlets and channels towards the more sheltered tidal mudflats. Recent work has revealed that superimposed upon these large-scale geomorphological gradients, ecosystem engineering biota can profoundly alter mud characteristics, promoting smaller-scale heterogeneity in sediment composition. While geomorphologists and engineers typically only consider large-scale geomorphological gradients in their sediment transport models, ecologists commonly study smaller-scale biophysical interactions while ignoring larger-scale geophysical processes. However, previous work has found that smaller-scale biophysical processes can interact with large-scale geomorphological processes to steer the larger-scale sediment transporting processes, which can in turn feeds back on benthic community composition. Yet, despite its potential importance, a multi-scale investigation of biophysical interactions is currently lacking as it requires extensive labor-intensive data collection and a solid integration of biota and sediment dynamics.