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.