The intensive use of limited water resources, the growing population rates and the various increasing human activities put high and continuous stresses on these resources. Major problems affecting the water quality of rivers, streams and lakes may arise from inadequately treated sewage, poor land use practices, inadequate controls on the discharges of industrial waste waters, uncontrolled poor agricultural practices, excessive use of fertilizers, and a lack of integrated watershed management. This study explores the impact of these pollution problems and the water quality degradation of irrigated agricultural watersheds. When the watersheds have a complex physical basis of interacting water bodies such as canals, drains and coastal lagoons as in the case of irrigated watersheds in coastal river Deltas, and when these environments are ‘data scarce environments’, the problems of managing water quality becomes more obvious and the need for reliable solutions becomes an urgent requirement.