The Florida snail kite (Rostrhamus sociabilis) is an endangered raptor that occurs as an isolated population, currently of about 2,000 birds, in the wetlands of southern and central Florida, USA. Its exclusive prey species, the apple snail (Pomacea paludosa) is strongly influenced by seasonal changes in water abundance. Droughts during the snail kite breeding season have a direct negative effect on snail kite survival and reproduction, but droughts are also needed to maintain aquatic vegetation types favorable to snail kite foraging for snails. We used a spatially explicit matrix model to explore the effects of temporal variation in water levels on the viability of the snail kite population under different temporal drought regimes in its wetland breeding habitat. We focused on three aspects of variations in water levels that were likely to affect kites: (1) drought frequency; (2) drought duration; and (3) drought timing within the year. We modeled a 31-year historical scenario using four different scenarios in which the average water level was maintained constant, but the amplitude of water level fluctuations was modified. Our results reveal the complexity of the effects of temporal variation in water levels on snail kite population dynamics. Management implications of these results are discussed. In particular, management decisions should not be based on annual mean water levels alone, but must consider the intra-annual variability.