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. These include: avoid using a river as the boundary of a PA; incorporate natural large-scale catchment processes into PAs; ensure that the water regimes of rivers, lakes, peatlands and groundwater-dependent ecosystems, as well as their linkages and interactions, are recognized and well managed within PAs and their catchments; avoid development of visitor infrastructure on priority freshwater ecosystems in PAs; encourage expansion of existing PAs to incorporate biodiversity hotspots, functional processes and connectivity; and promote new PAs for the last remaining free-flowing rivers and other high priority freshwater ecosystems.