Two-dimensional simulation of highly heterogeneous domains, especially those with disparate length scales, roughness conditions, and geometries, often leads to challenges such as long computation times and numerical instability. Simulation of challenging domains is often needed to guide flood management and environmental regulation agencies in operation and potential domain modifications. This work evaluates the ability of a two-dimensional unsteady hydrodynamic model to represent long-duration transient flows over a domain with highly heterogeneous roughness, geometric characteristics, and length scales through bed roughness representation. The domain includes 13km of Cache Creek and the 14.5km(2) Cache Creek Settling Basin, which traps both sediment and mercury. Calibration under different bed roughness methods, validation, and modeling results of bathymetric modification scenarios are presented. The modeling approach's performance supports its application as a tool for management of similar domains, such as settling basins, leveed floodplains, and reservoirs. Accurate representation of flow dynamics can also inform environmental management that involves transport of sediments, nutrients, and heavy metals. This study found that a two-dimensional unsteady flow model can accurately represent long-duration transient flow in a large settling basin with highly heterogeneous characteristics without parsing of the domain or flow events simulated.