Coastal phytoplankton blooms can result from upwelling of colder nutrient-rich water, seasonal fluvial or anthropogenic point sources of nutrient. Here we analyze 15-year time series of monthly mean and 8-day satellite-derived chlorophyll-a (Chl-a) and sea surface temperature (SST) on the southern Queensland continental shelf (24.25–28.25°S) from March 2000 to February 2015. We examine the interannual variability in these parameters and its relationship to algal bloom dynamics. Seasonal climatological means are computed and analyzed. Empirical orthogonal function (EOF) analysis is applied to these time series. Cross-correlation and spatial correlation analyses are used to investigate the relationship between the multivariate ENSO index (MEI), Chl-a and SST. Computed eigenvectors of the time series of Chl-a and SST present a strong seasonal variability on the first EOF modes. Thus, the seasonal variability was removed by computing monthly and 8-day Chl-a and SST anomalies. The EOF analysis was then applied to the anomaly time series. Correlation analysis results show a positive correlation between MEI and the eigenvector of the first EOF of the monthly Chl-a anomaly with time lag of three to four months. We find a negative correlation between MEI and the eigenvector of the second EOF of the monthly Chl-a anomaly with time lag of three to four months. There is no correlation between MEI and eigenvectors of the monthly SST anomaly. There are significant correlations between eigenvectors of the first and second EOF modes of 8-day Chl-a and the first and second EOF modes of 8-day SST respectively. Negative correlation coefficients between 8-day anomalies of Chl-a and SST are found on the continental shelf to the east of Fraser Island and Stradbroke Island. Analysis of a particular algal bloom event indicates a negative SST anomaly and negative curl of wind stress in the waters to the southeast of Fraser Island suggesting that wind stress is possibly a secondary but significant physical driver of the upwelling system. Our results suggest that variability in phytoplankton biomass on the southern Queensland continental shelf is driven by upwelling of nutrients during the spring dry season and fluvial nutrient loads during the summer and autumn wet seasons. Seasonal change is the primary factor controlling the variability of Chl-a and SST while climate variability (ENSO) and upwelling are secondary but significant factors.