Moult, the process of replacing old feathers with new, is a critical event in the annual cycle of all bird species. In the Curonian Lagoon, situated in the south-eastern Baltic Sea, recreational activities and shipping lanes occur in close proximity to the staging areas of waterfowl. Knowledge on the habitat use of these birds however is scant. In this study, we combined visual observations, satellite telemetry and the distribution of macrophytes to study habitat use by moulting herbivorous mute swans (Cygnus olor) and analysed how the localities of the swans depended on the distribution of macrophyte habitats and anthropogenic activities. Our data highlighted the most important swan staging areas within the Lithuanian part of the Curonian Lagoon, this specifically being mostly shallow areas (<1-metre depth) with diverse and high-density coverage of submerged vegetation dominated by charophytes and pondweeds. The submerged macrophyte habitats in water depths of 1–2 m and stands of clasping-leaf pondweeds were considered less important for swans. Our results showed that mute swans exploited only half the most suitable habitat areas for feeding. Based on indirect assessment of the relationship between the abundance of swans and disturbance by kitesurfing and boating, we discuss possible impacts on their moulting grounds. Knowledge on both selection of moulting grounds and habitat use by waterbirds is necessary for effective management and biodiversity conservation.