Many adverse environmental factors influencing the Shatt-al Arab River, southern Iraq, during the past century and especially in recent years, combined with the ever-increasing demand for freshwater in the region, indicate the need to obtain information about its salinity regime. The aim of our study was both to find out what historical data there are and then to compare these with the results of a survey of the salinity and water quality of a stretch of the present river over the year October 2009–September 2010. The evidence suggests that there has been a marked upstream shift in the influence of sea water. Salinity values of 2 and 8‰ were found at two sites where elevated salinity had never been reported previously. Water quality variables indicated increased concentrations over the previous four decades and were beyond the national and international standards. As such changes in a major water resource have serious implications for the inhabitants of Basrah, the biological diversity in the river and the whole Gulf ecosystem, it is suggested that there should be a much more detailed study to provide the evidence needed to convince upstream water users of the need to conserve water and manage the whole catchment properly.