Constituents such as sediment, nutrients, and heavy metals carried by rainfall-runoff from urban surfaces pose an ecological threat to receiving water bodies and are thus increasingly regulated. Best management practices such as wet basins, hydrodynamic separators, and various “green infrastructure” unit operations are designed in part to separate constituents of concern from stormwater. The design, analysis, and implementation of such systems, particularly innovative and unproven ones, requires a robust model capable of accurately predicting constituent load reduction given site specific conditions. Many traditional empirical models assume that best management practices behave as idealized continuously stirred or plug flow reactors, and reduce constituent concentrations through first-order decay. While useful and historically necessary given a lack of alternatives, this modeling approach has limited practical benefit in the design and implementation of innovative control systems, and requires site-specific calibration to produce accurate predictions of load reduction. A physically-based, fundamental modeling approach has the potential to allow for improved design and watershed planning as well as improved accuracy and robustness of pollutant transport simulation. Computational fluid dynamics has been applied to simulating constituent transport and fate within stormwater unit operations in an effort to understand fundamental mechanisms, optimize design by improving volumetric utilization and providing performance predictions of design alternatives, and develop updated models for use in watershed planning. Recent modeling developments and applications are presented alongside design examples that demonstrate present challenges and future solutions.