The aquatic vegetation in 44 similar shallow and sheltered inlets exposed to different kinds of disturbances by boating was studied in a rocky archipelago in the Baltic Sea. The results indicate that both recreational boating activities and traffic by medium sized ferryboats may cause significant changes in community composition and have significant negative effects on species richness and the development of the macrophytic vegetation at greater depth. Changes in inlet morphology by dredging and increases in resuspension and turbidity by wave-action from boats were most probably the major factors contributing to the demonstrated differences in the vegetation between inlets. In inlets used as harbours for private boats (marinas) or adjacent to ferryboat routes, vegetation cover and species richness declined significantly more with depth than in reference inlets not exposed to disturbance by boating activities. In marinas, turbidity was significantly higher than in reference inlets. Accordingly, a canonical correspondence analysis showed that the abundance of species sensitive to poor light conditions, such as Chara spp. and Ruppia spp. were negatively correlated with marinas while Myriophyllum spicatum and Ceratophyllum demersum that are common in nutrient rich turbid habitats were positively correlated with marinas. Mechanical disturbance by propellers may also have contributed to the results, disfavouring Potamogeton pectinatus compared to similar caulescent species in marinas. Chara tomentosa and Najas marina that are exposure sensitive mud thriving species were negatively correlated with inlets adjacent to ferryboat routes, while the macroalga, Fucus vesiculosus that is dependent on clean substrate for successful recruitment was positively correlated with inlets adjacent to ferryboat routes. It is important to explore further the effects of boating activities in these habitat types, since the studied inlets sustain a high diversity of both plants and invertebrates and provide highly significant recruitment areas for coastal fish in the Baltic Sea. (C) 2004 Elsevier Ltd. All rights reserved.