We studied the effects of boating and navigation activities on the recruitment of coastal fish in the Stockholm archipelago in the NW Baltic proper. The impacts were quantified by sampling metamorphosed young-of-the-year (Y-O-Y) fish in inlets adjacent to i) routes for medium-sized passenger ferries; ii) berths (small marinas) with small boats; and iii) references. Species with high preference for vegetation were negatively influenced by boating and navigation activities and species with low preference positively influenced. Pike (Esox lucius) Y-O-Y were significantly more abundant in reference areas, while bleak (Alburnus alburnus) were more abundant in dredged marinas. No statistically significant patterns were identified for perch (Perca fluviatilis) although there was a trend of low abundance along ferry routes. Many species of nearshore fishes are dependent on submerged vegetation as spawning and larval substrate, structural refuge and feeding habitat. Our results suggest that the negative effects from boating and navigation activities on the coverage and height of vegetation, especially on species of Chara and Potamogeton spp., may contribute to changes in the Y-O-Y fish community.