Maturation ponds are used for the treatment of wastewater and often form part of a municipal water treatment system. The primary purpose of a maturation pond is to disinfect pathogenic organisms present in the wastewater. Current knowledge of the disinfection mechanisms attributes ultraviolet radiation from sunlight as the most significant factor affecting die-off in maturation ponds. However, these artificial ponds are shallow ( 1m) and open to the atmosphere. This presents complex dynamics arising from climatic interactions at the water surface, in-water spatial effects from attenuation of sunlight, spatial distributions of pathogenic organisms, and the coupling effects of thermal gradients to turbulent dispersion. These interactions form a typical diurnal cyclic pattern, and as such have been segregated in previous studies. There exists a gap in the literature in understanding the effects and implications of the coupling between disinfection and hydrodynamics when transient and spatially applied sunlight is present. Experimental and modelling methods were used to evaluate the diurnal patterns of Escherichia coli die-off, natural mixing and their effects. Experimentally, an operational maturation pond was studied in the South East Queensland region of Australia. Extensive data for the pond was recorded. To investigate the coupling dynamics and implications of assumptions, the system was modelled by completely stirred tank reactor (CSTR) zero-dimensional, one-dimensional, and two-dimensional computational fluid dynamics (CFD) approaches. In modelling the maturation pond, the transport equations for E. coli featured a source term with disinfection kinetics included as a function of local ultraviolet radiation intensity. Within the literature, several sunlight disinfection terms were identified and tested in the models against our set of experimental data. The maturation pond was found to stratify and completely destratify in a diurnal cycle. E. coli concentrations were observed to fluctuate in the near surface region and follow the diurnal cycle of high daytime die-off and increasing concentrations into night time and early morning. It was hypothesised that localised ultraviolet radiation and stratification caused the large daytime concentrations and night-time natural convection was responsible for the increasing night-time concentrations of measured E. coli concentrations. The results of the model simulations showed that in the occurrence of stratification, disinfection was primarily restricted to the near-surface region. The significant implication is that concentrations beneath the near-surface region are not disinfected during daytime. Experimental E. coli concentrations also supported this. Both the practical one-dimensional model and two-dimensional CFD simulations featured this phenomena. However, due to the CSTR model assumptions, daytime die-off was not as pronounced and less than experimental data. Similarly, the CSTR model exposed all concentrations to sunlight during daytime, and therefore CSTR night-time concentrations were greater than the distributed models. Further validation is required. To improve the coupled hydrodynamics-disinfection modelling, a two-dimensional CFD simulation was carried out. To determine the effects of turbulence, five common turbulence models were simulated and evaluated in addition to a laminar flow model (run on the same computational mesh to highlight the effects of removing turbulence terms). The results of the CFD simulations showed that turbulence can have a marked impact on predictions and both horizontal and vertical mixing is important. In terms of thermal stratification, all turbulence model choices gave results that were similar enough to render a no-difference decision. Prior to this thesis, it was simply assumed that thermal effects were small for disinfection in maturation ponds, however this work has demonstrated that there are two key thermal mechanisms influencing mixing and subsequently pathogen die-off. The first of these is simply free convection resulting from water surface cooling which appears as a body-force term in the Navier-Stokes equations. The second, and more subtle mechanism, is the effect that temperature/density gradients have on suppression or enhancement of turbulence in the pond. To investigate this effect, CFD simulations were run with and without turbulent buoyancy production terms in the turbulence models. The effect was so pronounced that it has become clear that inclusion of buoyancy production in the turbulence model is more significant to mixing and pathogen disinfection than the choice of the turbulence model itself. Very few previous researchers modelling maturation ponds have even included spatial temperature gradients in their analyses. In contrast, this thesis has demonstrated that thermal mixing is essential for effective sunlight disinfection to occur in maturation ponds and for providing guidance to the design of maturation ponds.