This paper discusses a research project dealing with the mapping of the intertidal vegetation of several harbours along the southern coastline of England. It describes in detail the methods used to map the vegetation and gives examples of the results from these studies. This paper then goes on to explain how these results are applied by the Environment Agency of England and Wales to improve water quality in the harbours. This type of vegetation mapping is useful in monitoring the development of the intertidal species including Spartina, Zostera and of particular importance to this study the green algae Ulva and Enteromorpha. The work was undertaken with funding from the Environment Agency and at present has taken place over a four year period. The data collected will be used by the Environment Agency to assess macro-algae cover values for the intertidal area of the harbours concerned. This forms part of the Agency's commitment to the EU Nitrates Directive and the Urban Waste Water Treatment Directive. Some of the species mapped act as suitable indicators of water quality and are symptoms of eutrophication. Other species are of interest for nature conservation and were recorded to provide a record for longer-term trends in vegetation patterns within the harbour. This paper aims to provide readers with an understanding of the techniques involved as well as an evaluation of the methodology.