The Hawkesbury–Nepean River System (HNRS) is one of the most important inland river systems in Australia, which supplies over 90% of Sydney's potable water. In this paper, 25 water quality parameters from nine sampling stations in the HNRS covering a period of 12 years are used to examine the trends in the water quality data in the HNRS. It has been found that there is an overall increasing trend of turbidity, chlorophyll-a, alkalinity, total iron, total aluminium, total manganese and reactive silicate, indicating an overall water quality deterioration in the HNRS during the last decade. The parameters such as phosphorus, suspended solids and ammonical nitrogen do not show any marked change over the period of study. Although an improvement in water quality can be seen at some stations downstream of the undisturbed parts of the catchment, there is a clear trend of increased chemical and physical water quality deterioration at many locations in the HNRS. Better land use planning is recommended to achieve an overall improvement in the water quality of the HNRS in future.