Summary 1. Climate change encompasses changes in both the means and the extremes of climatic variables, but the population consequences of the latter are intrinsically difficult to study. 2. We investigated whether the frequency, magnitude and timing of rare but catastrophic flooding events have changed over time in Europe’s largest estuary. Subsequently, we quantified how this has affected the flooding risk of six saltmarsh nesting bird species. 3. We show that maximum high tide has increased twice as fast as mean high tide over the past four decades (0·8 vs. 0·4 cm year−1), resulting in more frequent and more catastrophic flooding of nests, especially around the time when most eggs have just hatched. 4. Using data on species’ nest elevations, on their timing of egg‐laying and on the duration that their eggs and chicks are at risk from flooding, we show that flooding risks increased for all six studied species (even after accounting for compensatory land accretion) and this is expected to worsen in the near future if they do not adapt. Moreover, our study provides the first evidence that increasing flooding risks have reduced the reproductive output below stable population levels in at least one species, the Eurasian oystercatcher Haematopus ostralegus. 5. Sensitivity analyses show that currently birds would benefit most from adapting their nest‐site selection to higher areas. However, historically the lower marsh has been favoured for its proximity to the feeding grounds and for its low vegetation aiding predator detection. 6. Synthesis and applications. We argue that it is more difficult for birds to infer that habitat quality has decreased from changes in the frequency of rare and unpredictable extreme events than from trends in climatic means. Consequently, at present the lower parts of the saltmarsh may function as an ecological trap. The creation of new (i.e. low) saltmarshes – currently a restoration priority – may thus counteract the goal of increasing the avian biodiversity of an area. Management tools to mitigate the effects of climate change, either by making the higher saltmarsh more attractive (mowing, predator control) or by reducing the flooding risk of the lower marsh (building elevated plots), await to be tested.