Despite 200 years of European settlement, the Hawkesbury-Nepean catchment sustains a rich and diverse fauna. This is a consequence of extensive sandstone environments largely unsuited for development that escaped the extensive habitat modifications affecting the fauna of the grassy woodlands on the Cumberland Plain and Southern Tablelands. The most significant impacts followed the clearing and fragmentation of the vegetation for agriculture. Changed fire regimes, the naturalization of exotic plants and animals, and disease were also factors in the decline of native birds and mammals. Data on frogs and reptiles are limited, but some reptiles have declined in abundance in association with the loss of habitats. Not all native species have been adversely affected by European settlement and a number of birds have increased in abundance and extended their range within the catchment. Agricultural clearing and urban development have also affected aquatic ecosystems. The pre-European environment was apparently characterized by creek and river systems subjected to periodic floods, but with clear water, low nutrient levels, and clean sandly or rocky substrates. Increased nutrient levels, turbidity and siltation associated with urban and rural effluents, land clearing, foreshore erosion and river bed mining has reduced the extent of seagrass communities in the lower Hawkesbury and changed the substrate of rivers and the estuary. Mangrove communities have expanded. Other impacts on aquatic environments include the removal of riparian vegetation and the draining of wetlands, changes of flow regimes, dredging of channels, pollution of water from domestic, industrial and agricultural sources, changes in salinity, eutrophication of wetlands and the over-exploitation of the aquatic fauna. In freshwater creeks and rivers the native fauna has declined in abundance, while introduced species have spread throughout the catchment. In estuarine and marine environments, the fauna associated with clear water, low siltation rates, and seagrass beds has declined and species that were formerly abundant are now scarce. The native terrestrial and aquatic fauna in the catchment will continue to decline with urban expansion and better management of human activities within the catchment is urgently required. Further clearing within the catchment is unwise and existing vegetation remnants (including freshwater wetlands) should be protected from development. This is particularly important on the Cumberland Plain and Southern Tablelands where as distinctive fauna is associated with vegetation remnants and the reserve system is inadequate. Similarly provision needs to be made for minimum freshwater flows into the Hawkesbury-Nepean estuary. Nutrient removal from sewage, control of stormwater runoff, and better management of agricultural chemicals, fertilizers and mining within the catchment is necessary to restore water quality. Foreshoes should be revegetated. Most importantly, urban expansion and population growth within the catchment should be restricted.