Recreational boating increases globally and associated moorings are often placed in vegetated habitats important for fish recruitment. Meanwhile, assessments of the effects of boating on vegetation, and potential effects on associated fish assemblages are rare. Here, we analysed (i) the effect of small-boat marinas on vegetation structure, and (ii) juvenile fish abundance in relation to vegetation cover in shallow wave-sheltered coastal inlets. We found marinas to have lower vegetation cover and height, and a different species composition, compared to control inlets. This effect became stronger with increasing berth density. Moreover, there was a clear positive relationship between vegetation cover and fish abundance. We conclude that recreational boating and related moorings are associated with reduced cover of aquatic vegetation constituting important habitats for juvenile fish. We therefore recommend that coastal constructions and associated boating should be allocated to more disturbance tolerant environments (e.g. naturally wave-exposed shores), thereby minimizing negative environmental impacts.