Sunlight disinfection is important for treatment of wastewater within maturation ponds. This study analyses the movement of Escherichi coli within a slice of a maturation pond, being affected by stratification, sunlight attenuation and mixing driven by wind shear and natural convection using computational fluid dynamics (CFD). Since the exposure to ultraviolet light is most effective in the near-surface region of the pond, natural convective mixing mechanisms to transport the pathogens from the lower parts of the pond are critical for disinfection efficacy. Different turbulence models are considered for closure of the momentum conservation equations and compared with a laminar flow simulation and a completely stirred tank reactor (CSTR) model. The effect of turbulence and stratification is shown to be significant for thermal and velocity distributions, and predictions of E. coli die-off. Greater volume-averaged E. coli die-off was predicted by the computationally convenient CSTR model than the CFD turbulence and laminar models. The simulation results are compared with experimental data and show that complete vertical mixing occurs in a diurnal pattern aiding die-off in sunlight-attenuating water. Practical applications of the model can assist in management strategies for maturation ponds such as off-take locations/times and evaluating seasonal variations in sunlight disinfection.