Freshwater is arguably one of Earth's most threatened natural resources, on which more than 7 billion people depend. Pressures on freshwater resources from infrastructure, resource development, agricultural pollution and deforestation are mounting, particularly in developing countries. To date, conservation responses such as Protected Areas (PAs) have not typically targeted freshwater ecosystems and their services, and thus little is known about the effectiveness of these efforts in protecting them. This paper proposes and pilots an innovative freshwater services metrics framework to quantify the representation of potential freshwater services in PAs under conditions of scarce data, with a pilot application for Cambodia. Our results indicate that conservation actions have more effectively represented potential freshwater regulation services than potential freshwater provisioning services, with major rivers remaining generally unprotected. Results from the framework are then used to propose a series of context and region specific management options to improve the conservation of freshwater services in Cambodia. There is an acute need for such management options, as the country's food security depends largely on important freshwater ecosystems such as the Tonle Sap Lake and the deep water pools systems of the Mekong River. The framework proposed can be applied in other countries or large river basins to explore the degree of representation of freshwater services within PAs systems, under conditions of sparse data.