The deterioration of estuarine and freshwater ecosystems in development areas such as Sydney is acknowledged as each level of government and by water managers and academia in Australia and is recognised as a major problem by the broader community. The key factors in the deterioration include development, a lack of strategic planning, loss of habitat, fisheries activities, shipping sewage waste and urban runoff.
The bay is subject to many legislative and planning requirements from State Government agencies and local councilswith responsibility for the waters and land within the catchment of Botany Bay. This maze of requirements, conditions and guidelines for encouraging better water resource and land use management practices is complex and often leads to a poor response to the challenge managers such as local government. Local government is however slowly taking up the challenge and members of the Sydney Coastal Councils Group in the catchments draining to Botany Bay are involved in numerous measures to protect and enhance it.