For better planning of a managed aquifer recharge (MAR) project, the most promising strategies should analyze the environmental impact, socio-economic efficiency, and their contribution to the existing or future water resource conditions in the region. The challenge of such studies is to combine and quantify a wide range of criteria from the environment and society. This necessity leads to an integrated concept and analysis. This paper outlines an integrated approach considering environmental, health, social and economic aspects to support in the decision-making process to implement a managed aquifer recharge project as a potential response to water resource problems. In order to demonstrate the approach in detail, this paper analysed several water resources management strategies based on MAR implementation, by using treated wastewater in the Northern Gaza Strip and the potential impacts of the strategies on groundwater resources, agriculture, environment, health, economy and society. Based on the Palestinian water policy (Year 2005–2025) on wastewater reuse, three MAR strategies were developed in close cooperation with the local decision makers. The strategies were compared with a base line strategy referred to as the so-called “Do Nothing Approach”. The results of the study show that MAR project implementation with treated wastewater at a maximum rate, considered together with sustainable development of groundwater, is the best and most robust strategy amongst those analyzed. The analysis shows the defined MAR strategies contribute to water resources development and environmental protection or improvement including an existing eutrophic lake. The integrated approach used in this paper may be applicable not only to MAR project implementation but also to other water resources and environmental development projects.