A number of relatively simple changes to the way protected areas (PAs) are designed and managed can help to further improve their conservation benefits for surface- and ground-water-dependent freshwater ecosystems and estuaries. The dual imperative of having to cooperate with multiple management agencies and stakeholders, and deal with multiple interacting and constantly changing threats add both a social and a biophysical layer of complexity to the task of conserving freshwaters. Under these circumstances, adaptive management seems to be gaining traction as an approach to management. Threats to rivers and freshwater biodiversity are increasing in many regions as human populations expand and seek higher living standards and improved quality of life. The natural environmental regimes that govern aquatic ecosystems, especially water regimes, have been replaced by altered regimes in many areas of the world under increasing human pressure for fresh water and in response to shifting climates.