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The aim of this paper was to analyse the spatial and temporal patterns and drivers of water quality in a large arid/semi-arid river system (River Murray, Australia) using a long term (1978-2015) dataset collected from 24 monitoring sites. The water quality is highly variable, but on average electrical conductivity (EC), pH, turbidity, dissolved and total nutrient, colour and chlorophyll a levels increase with distance downstream from the headwaters to the lower reaches. This is a function of the natural accumulation of dissolved and particulate components and intermittent, mostly diffuse source, pollutant inputs. The Darling tributary inflow increases turbidity, total phosphorus and pH in the main River Murray channel. Based on long-term trend analysis at four representative sites, EC, nutrients and colour showed declining trends on average at most sites except in the headwaters. Increased flow increases concentrations of most quality parameters, although at very high flows decreases in pH, EC, turbidity and oxidized nitrogen were apparent at many sites. The extreme Millennium drought (2002-2009) period resulted in lowered concentrations of many water quality parameters, indicating retention in the landscape. In the post-drought flooding (2010-2012) period a large amount of organic material was mobilised, resulting in much higher peak colour concentrations than when mid-range flooding was more frequent. It is critical that this monitoring program is continued as a Basin-wide water management plan is implemented.