Large eddy simulation (LES) and coupled physical laboratory-scale modeling are performed to elucidate tracer transport and particulate matter (PM) fate in a baffled clarification system. Such baffled systems are common for urban water unit operations and processes. Flow hydrodynamic indices of these systems such as short-circuiting are often examined with measurement of inert tracer transport as a surrogate for chemical or PM transport and fate. Results of this study illustrate complex interactions between turbulent flow, tracer, and various PM diameters at the system scale. PM preferential accumulation and the discordance of PM transport with respect to flow hydrodynamics are observed based on the modeling results; otherwise not practical with physical model testing. Results demonstrate that baffling can promote system tracer mixing and improve volumetric utilization by extending the mean flow path through flow separation and bifurcation. The baffle tested produced high turbulence kinetic energy near the sedimentation floor and reduced PM separation (clarification) as compared to the unbaffled system used as a control. The unbaffled system in this study yields the highest PM separation, even though significant short-circuiting occurs during the residence time distribution (RTD) of the tracer. Further analysis demonstrates the mechanistic difference between the tracer transport and the finer suspended PM as compared to larger settleable and sediment PM diameters. Results illustrate that the tracer RTD, residence time (RT) and hydraulic efficiency indices are not reliable surrogates for PM or PM-bound chemical/pathogen separation. In addition, simulations suggest a site, system or condition-specific design approach given the coupled dependence on flow and design geometry.