Hydraulic performance of clarifiers in water and wastewater treatment plants significantly affects the settling efficiency of suspended particles. Structural and ambient parameters can deteriorate this performance. Through a verified three dimensional numerical study, we evaluated hydraulic performance and settling efficiency in a rectangular clarifier with a nominal hydraulic retention time (HRT) of 1 h and options for structural baffles with angles of 20°, 30°, 45° and 70°. Large eddy simulation and Lagrangian particle tracing were used to trace particles 80 to 850 μm in diameter. A passive scalar tracer study was conducted to reveal discrepancies in nominal and real HRT. By posing a 5 m/s wind, ten different scenarios were simulated. The wind caused 17% and 6% reduction in HRT and settling efficiency, respectively. Baffles improved these indicators with the 45° baffle showing the best performance with an approximate settling efficiency of 93%. The study highlighted the importance of using baffles, in particular for small size particles for which influencing factors such as wind deteriorate their settling efficiency.