Observational evidence from recent studies reveals that the water quality in the Great Barrier Reef (GBR) has declined due to excess river discharge of terrestrial pollutants derived from adjacent catchments, highlighting the need to monitor water quality at the mouth of each GBR catchment. While remote sensing based approaches have shown promise in monitoring water quality in open ocean and inland waterbodies, it is challenging to extend their applications in the tidal-affected estuarine water. This study aimed to advance our understanding of water quality at the spatiotemporally dynamic Fitzroy Estuary and Keppel Bay regions, with timeseries Landsat-8 OLI observations that have a high spatial resolution of 30 meters. A deep learning model was trained and validated with biophysical modelling and in-situ water quality measurements. The model was then applied to Landsat-8 images for generating timeseries maps of total suspended solids (TSS), dissolved organic carbon (DOC), and chlorophyll. Our results revealed the spatiotemporal patterns of TSS, DOC, and chlorophyll at the Fitzroy Estuary and Keppel Bay regions, providing support to the estimate of terrestrial pollutants from the Fitzroy catchment to the GBR region.