Multiple stresses are putting great pressure on water resources systems. Population growth, climate change, prosperity, energy production, food crisis, and water governance are among the factors straining water resources. Decision makers from rich to poor countries and from commercial to non-governmental organisations are struggling to devise schemes to adapt to these stressed water conditions. Better efficiency for water resources systems, and particularly irrigation systems, is recommended as one of the most important responses to climate change, unsustainable development, and water shortage. However, using certain efficiencies such as Classical Efficiency caused systems not to perform according to decision makers’ objectives. Effective Efficiency is a robust composite indicator that includes in its formulation both a flow weight, taking into account the leaching fraction, and reuse of return flows. Classical Efficiency is defined as the percentage of the diversion consumed beneficially, such as by crop evapotranspiration. Effective Efficiency, on the other hand, is defined as the ratio of beneficial consumptive use to total consumption, expressed as a percentage. In this paper, a normalised and non-dimensional form of Effective Efficiency is developed and necessary constraints for its successful application are explained. These constraints express water balance, flow weights and their thresholds, water reuse, and total consumptive use. Basic guidelines are proposed for better decision making in determining possible interventions for improving Effective Efficiency. This is done by analysing its domain through analytical and graphical methods. Three real cases are considered, namely, Imperial Irrigation District and Grand Valley irrigation systems in the United States and Nile Valley in upper Egypt. Three-dimensional sensitivity analysis is performed on Effective Efficiency and its variables using the three cases. This leads to an examination of the validity of the analysis and to suggestions for better intervention options. Meanwhile, it is also shown why Classical Efficiency should be used with care.