This study developed and applied dynamically-integrated MIKE21 Flexible Mesh hydrodynamic, wave, sediment transport and morphology, and particle tracking models to analyze the effect of sediment impoundment basins and Intracoastal Waterway (IWW) channel rerouting near Bakers Haulover Inlet in Miami-Dade County, Florida, USA. The study aims to find alternatives that reduce shoaling and IWW channel maintenance dredging cost. For computational efficiency and to complete the alternative evaluations within schedule, the study used a month-long representative period from a representative year to estimate shoaling rates and then prorated the computed shoaling rates for an average year. The prorated shoaling rate offers a good approximation of the shoaling rates of channel shoaling reduction alternatives relative to the shoaling rate for baseline (existing) conditions. Model results show the best performing shoaling reduction alternative requires maintenance dredging once every eight years and provides a substantial annualized cost savings of $249,000 when compared with the baseline dredging frequency of once every four years. The cost of this study (including data collection, integrated modeling, and related analysis work) is a very small percentage (1%–2%) of the total cost savings with the implementation of any of the viable shoaling reduction alternatives.