In the Mediterranean countries, agriculture poses challenges in terms of its production expectations, resources availability, pollution, general management and implementation of economic tools (e.g. full cost of irrigation water, according to the Water Framework Directive). This study attempts to provide useful approaches for small water supply agencies facing multiple management, funding, environmental, and practical issues. A representative case in Central Greece is examined, in order to describe the situation in understandable terms supporting sustainable management. Simple hydro-economic tools were used to address these challenges; water balance, profits from agriculture, water value, water quality, management strategies, and full cost of irrigation water were simulated and incorporated into a Decision Support System (DSS), using Multi-Criteria Analysis (MCA), involving experts on water resources management and local policymakers. This is the first hydro-economic study designed for a Greek rural agency, aiming to improve and encourage integrated monitoring and management at multiple levels, communicating more efficient water use approaches to local irrigation management communities.