The Zlivsky pond (vicinity of České Budějovice, South Bohemia, Czech Republic) belonged to the most important breeding places for three species of wading birds: of up to 100 pairs of the night heron (Nycticorax nycticorax), which is one third of the South Bohemian population of this species, of 3 pairs of spoonbill (Platalea leucorodia), also one third of the Czech spoonbill population, and of 1–4 pairs of little egret (Egretta garzetta), which occurred here since 1997 as in the first and only site in Bohemia. All three species are included among the NATURA 2000 selected target species. The water level in the pond markedly increased during the flood in August 2002 and the islands were flooded for about 3 weeks. In 2003, the year following the flood, only two unsuccessful breeding pairs of the spoonbill were recorded, while the other two species were absent, although no direct deaths of birds due to floods were observed. Here we analyse the mechanism that led to disappearance of these rare bird populations. We found that the most likely cause for that was disappearance of almost all the small (less than 4 m in height) black elder (Sambucus nigra) shrubs suitable for breeding of these species. These findings may aid future efforts to save these rare bird species.