The inner continental shelf is a complex environmental system marked by sharp variations in bed roughness. Such heterogeneous systems account for 80% of the non-rocky inner shelves worldwide. Interactions among forces (waves, tides, turbulence, and bioturbation) and roughness elements (bed forms, rocks, and anthropogenic objects) exert major controls on sedimentary processes. This study attempts to advance the knowledge and understanding of the morphodynamics of the inner shelf. This study investigates scour and morphodynamic processes at Tairua, New Zealand; Cedar Island, Virginia; Indian Rocks Beach, Florida; and Beaufort Inlet, North Carolina. Using data from the field, the study develops new conceptual models to characterize and quantify the hydrodynamics and morphology of the seabed. The overall dataset includes side-scan sonograms, sub-bottom profiles, grain-size analyses, suspended sediment concentrations and hydrodynamic measurements. Analysis of the morphological data yielded a six-type classification of bottom features previously termed Rippled Scour Depressions (RSDs). The observed stratigraphic signature of RSDs does not agree with the previous interpretation of their formation. Striking spatial and temporal variations in seabed roughness produce significant enhancements of hydraulic roughness and turbulence over different substrates resulting in a self-organized, feed-back system of erosion (scour), deposition, and modified bed forms. The study demonstrates that widely used ripple models inadequately predict bed form geometry and behavior, especially during storms. Improved understanding of scour processes developed in this study leads to a new model of scour and burial of sea-bed objects such as naval mines and archaeological artifacts. When using the model to predict scour and burial, the greatest errors result from the uncertainties in the available forecasts of wave conditions. The model includes vertical variations in sediment characteristics as field observations indicate abrupt changes in substrate substantially alter the scour process. The overall study makes substantial contributions to the general understanding of RSD behavior by tying together detailed field studies with applicable insights from the area of complexity research. A new conceptual model of complex phase-transition is developed, involving critical process factors (hydrodynamics, underlying geology, and depth), which contribute to the observed spatial complexity and temporal variability of different RSD types