A multi-year ocean glider dataset, obtained along a representative cross-shelf transect along the Rottnest continental shelf, south-west Australia, was used to characterise the seasonal and inter-annual variability of water column properties (temperature, salinity, and chlorophyll fluorescence distribution). All three variables showed distinct seasonal and inter-annual variations that were related to local and basin-scale ocean atmosphere processes. Controlling influences for the variability were attributed to forcing from two spatial scales: (1) the local scale (due to Leeuwin Current and dense shelf water cascades, DSWC) and (2) the basin scale (El Nino-Southern Oscillation, ENSO, events). In spring and summer, inner-shelf waters were well mixed due to strong wind mixing, and deeper waters (> 50 m) were vertically stratified in temperature that contributed to the presence of a subsurface chlorophyll maximum (SCM). On the inner shelf, chlorophyll fluorescence concentrations were highest in autumn and winter. DSWCs were also the main physical feature during autumn and winter. Chlorophyll fluorescence concentration was higher closer to the seabed than at the surface in spring, summer, and autumn. The seasonal patterns coincided with changes in the wind field (weaker winds in autumn) and air-sea fluxes (winter cooling and summer evaporation). Inter-annual variation was associated with ENSO events. Lower temperatures, higher salinity, and higher chlorophyll fluorescence (> 1 mg m(-3)) were associated with the El Nino event in 2010. During the strong La Nina event in 2011, temperatures increased and salinity and chlorophyll fluorescence decreased (<1 mg m(-3)). It is concluded that the observed seasonal and inter-annual variabilities in chlorophyll fluorescence concentrations were related to the changes in physical forcing (wind forcing, Leeuwin Current, and air-sea heat and moisture fluxes).