The coastal focus and beach culture of Australia’s population in general, and the people of New South Wales in particular, mean that coastal systems are both highly prized and subjected to great pressures. The vast majority of the wastewater generated by the 7.3 million people of New South Wales is discharged directly to the ocean. The dispersion and fate of waterborne pollutants and their potential to impact coastal ecosystems are fundamentally determined by the dynamics of the coastal boundary layer (CBL). This turbulent interface between the coastline and the deep oceans is defined and classified for the first time in this thesis. Coastal morphologies and changes in the orientation of the coastline promote turbulence and strong gradients with extreme variability and heterogeneity over a broad range of scales. Conceptual models are presented to characterise New South Wales coastal boundary layer processes. The broad aims of this thesis are to investigate the coastal boundary layer processes that affect dispersal and advection of pollutants, and to develop conceptual models and tools to facilitate coastal management. Remote sensed ocean colour and sea surface temperature observations define meso-scale CBL phenomena, and this study demonstrates their application to support management decisions in relation to marine algal (phytoplankton) blooms. However, considerable scope exists to improve regional algorithms to deliver better ocean colour products for the optically complex (Case 2) waters of the inner coastal boundary layer. Past failures to consider the CBL (morphological) settings of pollutant discharges to coastal waters have led to inefficient pollutant discharge systems and potential environmental impacts. Two case studies, investigate the principal forcing mechanisms and demonstrate the importance of morphology in controlling the dispersion and retention times of pollutants. The first case study is focused on Sydney coastal waters where pollutant loadings are greater in magnitude and different in character than elsewhere in New South Wales. Here population pressures generate large wastewater loadings but the distances to offshore discharge locations are large compared to the scale of coastal roughness (headlands and bays) and the water is deep, thus reducing the risk of local retention of pollutants and increasing the potential for rapid dilution. By considering simulations of near field effluent plume behaviour in relation to long term ambient nutrient patterns specific periods of the year and depth intervals have been identified when outfalls would have an increased opportunity to influence bloom development, especially the upper half of the water column during late summer. However, algal blooms appear to be principally driven by seasonal oceanic nutrient enrichment. The research presented in this thesis, together with companion research previously published by the author and routine ongoing monitoring, indicate the viability of disposal of the Sydney’s excess sewage effluent (after source control and re-use options have been exhausted) via existing deepwater outfalls. In contrast, inner CBL settings with coastal irregularities (e.g. headlands and bays) have a greater propensity to trap pollutants. A new hydrodynamically relevant morphological classification of New South Wales bays, headlands and islands provides both broad context for case studies and guides preliminary assessments for other locations. This classification reveals a borderline propensity for flow separation and re-circulation in the lee of Corambirra Point which is the focus of the second case study off Coffs Harbour in northern NSW. Direct observations and 3D finite difference hydrodynamic (Eulerian) and particle tracking (Lagrangian) model simulations quantify transient re-circulation associated with local current accelerations and a persistent shear zone located in the wake to the south of Corambirra Point. The flux of ambient water across the prescribed outfall alignment increases eighteen fold, over a shear zone spanning a cross-shore distance of just 1.4km (from 1.6km to 3km offshore). In contrast, the potential for re-entrainment and trapping of effluent in transient re-circulation cells was demonstrated to be insignificant. The proposed location of the outfalls was 1.5km offshore whereas the greatest gain per unit extension of the proposed discharge point coincides with the centre of the shear zone located ~2km offshore. These case studies illustrate specific coastal boundary layer effects and indicate how an understanding of the spatial and temporal scales of these effects can be used to target more specific assessments of potential pollutant impacts. Simple morphological risk assessment tools are also presented to identify factors and processes which limit the exposure of sensitive environments to high pollutant concentrations and loads. Eddy retention effects are generally not incorporated in existing near field models but potential re-entrainment effects in wake zones can be assessed through the eddy retention value, which is introduced in this thesis. Although the approach presented here is focused on New South Wales coastal waters, the framework serves as a basis for general application elsewhere, and as a foundation for further refinement for application to NSW coastal waters. Existing scientific literature indicates that coastal boundary layer processes also shape the distributions of the biological species and communities. This further motivates the development of a process based understanding of coastal boundary layer dynamics as a fundamental platform to support environmental protection and biodiversity conservation initiatives.