Highlights
► We model secondary facultative wastewater treatment ponds with 3D hydrodynamics. ► Water quality processes were based on the Activated Sludge Models (ASM) concept. ► Baffles and wind have no effect when water quality is modelled mechanistically. ► But baffles and wind improve effluent quality when first-order processes are used. ► First order decay not appropriate to describe biochemical processes in a pond.