1. The distribution of submerged macrophytes along 20 km of lake shore (Lake Geneva, Switzerland) was compared between the years 1972, 1984 and 1995. Lake Geneva underwent rapid eutrophication until 1980, followed by reversal that is still in progress. Potamogeton pectinatus, P. perfoliatus, P. lucens and Elodea canadensis showed no significant changes in their distribution, with the two former species dominant throughout. Chara sp., and to a lesser degree Myriophyllum spicatum, decreased in abundance between 1972 and 1984 but had increased again by 1995. The abundance of P. pusillus increased regularly, while Zannichellia palustris and P. crispus almost disappeared from the study area. Elodea nuttallii was observed for the first time in Lake Geneva in 1995. 2. Two methods of bioindication of water quality by macrophytes are compared. The macrophyte index proposed by Melzer (1988) is based on nutrient load, whereas the saprobic index proposed by Sladecek (1973) measures organic pollution. The saprobic index is sensitive to small changes in species composition and abundance, and also reflects better the changes in eutrophication. It may therefore be a better bioindicator. 3. Geographic Information Systems (GIS) are useful for mapping and storing information on submerged vegetation allowing easy interrogation, updating and plotting of spatial information at various scales, and providing a reference for future comparisons.