<p>A multiyear, 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. Local and basin-scale ocean–atmosphere processes also affected the spatial distributions of the water column properties. The controlling influences for the variability were derived from (a) at the local scale, the Leeuwin Current and dense shelf water cascades (DSWC); and, (2) at the basin scale, the El Niño Southern Oscillation (ENSO). In spring and summer, shallow waters were well mixed due to strong wind mixing and the deeper waters (> 50 m) were vertically stratified in temperature that contributed to the formation of a subsurface chlorophyll maximum (SCM). With the onset of storms in late autumn, the water column was well mixed with the SCM absent. 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 sea bed 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<sup>−3</sup>) were associated with the El Niño event in 2010. During the strong La Niña event in 2011, temperatures increased (a <q>marine heat wave</q>), and salinity and chlorophyll fluorescence decreased (< 1 mg m<sup>−3</sup>). These changes were mainly associated with changed to the strength of the Leeuwin current. Over subsequent years, the temperatures gradually decreased, the salinity increased, and the chlorophyll fluorescence continued to decrease (< 0.25 mg m<sup>−3</sup>). These changes were mainly associated with an increase in the strength of the Leeuwin current that transported warmer, lower salinity, low nutrient water into the region. In the autumn of 2014, the chlorophyll fluorescence increased (> 1 mg m<sup>−3</sup>). It is concluded that the observed seasonal and inter-annual variability in chlorophyll fluorescence concentrations were related to the changes in physical forcing (wind forcing, Leeuwin Current and air–sea fluxes).</p>