Field measurements and numerical modelling of the shallow coastal waters offshore in south-western Australia were used to describe changes in the water column's vertical structure and the biological response on temporal scales of the order of hours and days. A cycle of chlorophyll a concentration, primary production, and photosystem II function on a diel timescale, which was related to changes in the solar irradiance and thermal structure, was identified. The diel cycle included (1) vertically well-mixed (or weakly linear) conditions in density and chlorophyll a early in the morning, resulting from vertical mixing through penetrative overnight convection; (2) depleted chlorophyll a concentration in the surface layer during the middle of the day due to photoinhibition; (3) an increased chlorophyll a concentration in the bottom layer by late afternoon due to optimum light conditions; and (4) the formation of a chlorophyll a break point (CBP) at the thermocline, which migrated downwards with the deepening surface mixed layer. On a longer timescale (days), moored acoustic instruments were used to derive echo level (EL), which approximated suspended particulate matter (SPM). Wind events ultimately controlled SPM, a conclusion based on (1) elevated EL during high windgenerated turbulence and bed shear stress, (2) positive time-lagged correlations between wind speed and EL at three field sites with different exposures to wave action, and (3) significant negative correlations between wind speed and depth-differentiated echo level (d(EL)/dz) at all sites. Sea breezes produced a similar response in EL through the water column to a small storm event, and wind-driven SPM resuspension resulted in a reduction in the sub-surface light climate (kd). Near-bed dissolved oxygen concentrations varied in accord with elevated wind speeds, EL and kd, highlighting a possible suppression of photosynthesis. One-dimensional modelling revealed that wind stirring was most often the dominant process in these waters. It was found that for a brief period during thermal stratification there was shear production of turbulent instabilities that migrated from the thermocline to the surface and the seabed. Convective cooling was not able to mix the water column entirely overnight without the addition of wind, and minimum wind speeds were determined for this complete vertical mixing. Bottom-generated turbulence was limited to a small region above the bed, and was deemed insignificant compared with mixing generated at the surface. Minimum wind speeds required for de-stratification and prevention of stratification were determined for summer, autumn and winter. A hypothetical desalination outfall was simulated for all seasons and it was concluded that positioning of the discharge at middepth was preferable compared to at the seabed. The results of this thesis advance the current knowledge of coastal biophysical oceanography and provide new insights into the temporal dynamics of the coastal water column of south-western Australia.

[Truncated abstract] This work was the first large-scale biological oceanographic study to be undertaken in the coastal eastern Indian Ocean adjacent to Western Australia, and covered both northwest (Exmouth Peninsula to the Abrolhos Islands) and southwest (Cape Naturaliste to Cape Leeuwin) regions. The study area was dominated by the Leeuwin Current (LC), an anomalous eastern boundary current that transports tropical water poleward and prevents deep nutrients from reaching the surface by creating large-scale downwelling. Indeed, LC and offshore waters were consistently associated with low nitrate concentrations and low phytoplankton biomass and production (< 200 mg C m-2 d-1). However, the physical forcing of the LC was offset, during the summer months, by upwelling associated with wind-driven inshore countercurrents (Ningaloo and Capes Currents), which provided a mechanism to access high nutrient concentrations normally confined to the base of the LC. ... Limited seasonal investigations off the Capes region of southwestern Australia showed that the winter production scenario can be very different than summer conditions, with strong Leeuwin Current flow that meanders onto the continental shelf and entrains seasonally nutrient-enriched shelf waters. However, production in the LC was still low (≤450 mg C m-2 d-1) due to light limitation resulting from both increased light attenuation and reduced surface irradiance characteristic of the winter months. This investigation provides fundamental knowledge on physical-biological coupling off Western Australia, with implications for fisheries management in view of seasonal and inter-annual variability in the strength of both the Leeuwin Current and inshore countercurrents.

[Truncated abstract] The expansion of human populations in coastal land margins has resulted in major modifcations to estuarine ecosystems. The use of numerical models as predictive tools for assessing remediation strategies is increasing. However, parameterisation of physical processes, developed mainly through field investigations, is necessary for these models to be reliable and effective management tools. The physical processes in micro–tidal diurnal tidal systems are relatively unknown and the current study examines field measurements obtained from the upper Swan River estuary (Western Australia), a diurnal, partially mixed system during the summer when the freshwater discharge is negligible. The aims of the study were to characterise, temporally and spatially, the dominant physical processes and associated sediment resuspension. Variability at three dominant time-scales were examined: 1) sub–tidal oscillations (∼5 to 10 days) resulting from local and remote forcing; 2) tidal (∼ 24 hours) due to astronomical forcing; and 3) intra-tidal (∼2 to 3 hours) resulting from the interaction between tidal constituents. Circulation in estuaries is widely accepted in the literature to be dominated, in varying proportions, by tidal range, freshwater discharge and gravitational circulation. In the upper Swan River estuary sub–tidal oscillations were responsible for the largest upstream displacement of the salt wedge in the absence of freshwater discharge. Moreover, these sub–tidal fluctuations in water level modified the ‘classic’ estuarine circulation. The dynamics of diurnal tides are largely controlled by the tropic month, which oscillates at a slightly different period to the lunar month, resulting in the spring–neap tidal cycle to be sometimes different from syzygy. The phase lag between the diurnal (O1 + K1) and semi-diurnal (M2 + S2) constituents, at the seasonal time scale cause the maximum tidal range to be near the solstice. Over a 24–hour tidal cycle this phase lag is manifested as an intra–tidal oscillation that occurs on the flood tide. Turbidity events that last ∼1 to 2 hours occur during the intra–tidal oscillation, but are not related to maximum shear stress predicted from the mean flow characteristics. The increases in turbidity during the intra–tidal oscillation is, however, correlated with the near–bed Reynolds fluxes. During the intra–tidal oscillation advection opposes the estuarine circulation in the near–bed region, promoting vertical shear that results in destratifcation of the water column. The turbulent mixing generated at the interface and in the near–bed region coincide with resuspension events. Similar turbidity data have often been disregarded and documented as being ‘spikes’ based on the premise that the mean flow was below a critical level to resuspend sediment. Resuspension events were not simply related to mean processes and may be controlled by turbulent instabilities generated when tidal currents reverse during an intra-tidal oscillation