The global growth of intensive livestock industries in the past two decades has raised significant concerns with regard to waste disposal strategies. Intensive livestock rearing represents highly concentrate point source of Green House Gases (GHG). A large potential impact is due to the substantial degradable fraction and the most common practice of anaerobic digestion in primary ponds causes the release of methane and carbon dioxide. One approach to capturing the biogas produced in treatment ponds is by covering the lagoons. Though anaerobic stabilisation ponds have been in use as treatment systems in Australian livestock industries for decades now, little is understood about the conversion mechanisms occurring within, and covering makes it more difficult to observe, analyse, and correct. There have been few attempts to evaluate the kinetic parameters associated with the degradation of these wastes. There are limited generalised input models, and very limited validation of existing models, particularly specific to Australian conditions. There is little understanding about the settling profiles and activity zones of the sludge accumulated in the ponds, functioning as primary anaerobic systems. Modelling of solids behaviour in stratified systems is very new and has not been attempted previously in conjunction with anaerobic conversion models. This thesis attempts to address these issues. Piggery effluent and feedlot manure samples were characterised and biochemical methane potential analysis was performed to assess their inherent degradation ability. It was found that effluent generating from sheds housing pigs at different growth stages had different degradability properties. In particular effluent from weaner, growing and finishing pigs degrade to a greater extent than their breeder counterparts and this is attributed to differences in industry management practices. In beef feedlots, over 40% of initial methane potential from manure is lost in 2-3 weeks of drying on pads and this loss is over 70% in stockpiles. There is significant reduction (up to 70%) in the non-degradable organic fraction of solids along with the expected reduction in the degradable fraction through the practice of stockpiling. To gain a better understanding of the processes in anaerobic lagoons, two Covered Anaerobic Lagoons (CALs) were monitored and lagoon performance documented. The CALs were modelled using computational fluid dynamics to describe the anaerobic digestion and predict the fluid flow and solids settling. This was achieved by lumping multiple components and solving in COMSOL multiphysics®. CAL performance (measured in VS removal and methane production) is subject to seasonal variation and is affected, among other factors, by the lagoon geometry, type of cover and type of piggery effluent treated. The distributed parameter models that were built based the two CALs describing the rate of reaction, were able to predict both flow and solids settling in the lagoon in a stationary solution. These models, while novel are preliminary explorations and provide opportunity to describe the multi-phase process kinetics in a dynamic environment.