In this study we investigated the interplay between water level management, floating macrophytic vegetation and nesting whiskered tern (Chlidonias hybridus) during 8 years (1995–2002) at a shallow macrophyte-dominated lake in western France. The specific question was to see if slight increases in the water regime of the lake (three scenarios), as part of a restoration programme, affect the timing of nesting and occupation of colonies by whiskered terns by way of changes in biomass of waterlily (Nymphaea alba) beds where colonies always establish. During the study period, egg-laying dates were progressively delayed up to 40–50 days (mid-May to early July) in relation to late appearance of suitable waterlily biomass (R2 = 0.67, p = 0.01) associated with high spring water levels (1.10–1.25 m vs. 0.95 m). Simultaneously some nesting attempts were observed in sub-optimal habitats (adjacent wet grasslands) in high flooding conditions leading either to poor breeding success or colony desertion. We concluded that there is a need for compromise between the experimental water levels used to control waterlily biomass and the nesting requirements of the whiskered tern population in this lake of international importance (260–510 pairs in 1995–2002, ‡ 1% Ramsar level).