This chapter describes the distinctive characteristics of freshwater ecosystems that must be considered when designing protected areas (PAs) in freshwater systems. It briefly describes the latest advances on how to integrate these ecological requirements. The chapter reviews some alternative approaches to conventional PAs that are being used to implement conservation efforts in freshwater systems and that could help enhance the implementation and effectiveness of conservation in freshwater systems. The last few years have witnessed a surge of novel ways to integrate these special needs of freshwater systems into well-established systematic conservation planning methods previously developed and widely applied in marine and terrestrial environments. Initiatives to improve or maintain the quality of drinking water, principally but not only for domestic use in municipalities, through land-based activities are expanding around the world and present an important opportunity for freshwater biodiversity conservation.