Activities and developments in the coastal zone, and in adjacent catchments, pose an increasing threat to the sustainability of the natural and socio-economic goods and services supplied by marine ecosystems. Governing authorities have had to develop new policies to promote environmentally responsible and sustainable development practices, either through legislation and/or incentive mechanisms. These, in turn, created the need for holistic and integrated frameworks within which to design and implement environmental management programmes. A structured ecosystem-scale approach for the design and implementation of marine water quality management programmes developed by the CSIR (South Africa) in response to recent advances in policies and legislation pertaining to sustainable utilisation of Southern Africa's marine environment is discussed. Keywords: Marine water quality, Ecosystem scales, Integrated management.