Coombabah Lake is a sub-tropical, semi-urbanised, shallow lagoon in southern Moreton Bay (Australia), recognised nationally and internationally as an important conservation and habitat zone. However, significant increases in urban development have occurred within the lagoon catchment in recent times, raising concerns over the sustainability of the lagoon ecosystem. This is typical of many estuarine environments which are ecologically and economically important waterways that often become surrounded by urban development and therefore experience degradation of water and sediment quality. The processes controlling the distribution of organic matter and nutrients in estuaries are especially important in understanding their chemical cycling. Consequently, the assessment and understanding of biogeochemical processes and other influential factors is essential for the effective management of estuaries. This study is a multi-disciplinary investigation of biological, physical, and biogeochemical processes occurring in the surface sediments and overlying waters of Coombabah Lake and the adjoining creek. The primary aim of this study was to investigate physico-chemical and biogeochemical processes occurring over various patial and temporal scales and improve the understanding of Coombabah Lake and similar shallow sub-tropical systems. Spatial variability of physico-chemical surface sediment variables and the sources and distribution of surface sediment organic matter were investigated to provide an understanding of the physico-chemical and ecological processes driving the lagoon system. Lagoon sediments were characterised by generally fine sediments with predominantly sandier sediments occurring within the northern region and muddier sediments occurring within the southern region. Although some sediment locations had elevated nutrient concentrations in comparison to adjacent lagoon sediments, nutrient concentrations within the lagoon were generally typical of Australian estuarine environments. Comprehensive analysis of biomarkers indicated that the lagoon received organic matter from a variety of autochthonous and allochthonous sources including terrestrial vascular plants (i.e. surrounding mangroves), diatoms, and benthic bacteria with the fringing mangroves potentially playing an important role in the lagoon food web. The intratidal variability of hydrological and physico-chemical variables were measured and the filterable nutrient and chlorophyll-a transport loads entering the lagoon determined. Instrumental measurements and hourly water collections provided the first account of intratidal variability within the system and indicated the lagoon and adjoining creek was characterised by a mixed tidal regime with cyclic and temporal variations in physico-chemical variables, suspended solids, and chl-a concentrations. Both dissolved oxygen and turbidity values exceeded regulatory guideline values for the region. Nutrient concentrations were typical of local and Australian estuarine environments and exceeded regulatory guideline values for the region. Nutrients sourced externally from the Coombabah Lake-Creek system resulted in increased transportation rates during flood events indicating a potential for increased nutrient loadings and enrichment within the lagoon and associated wetland environment...