Climate change and sea-level rise pose an imminent threat to the survival of coastal ecosystems, but the mechanisms by which animals inhabiting these areas may be affected by these changes are not well studied. During 2007–2009, we quantified the frequency of nest-flooding events at two salt marshes located in the northeastern United States that are of global importance to Saltmarsh Sparrow (Ammodramus caudacutus) conservation. Although nest flooding is a major cause of nest failure in this species, we lack a detailed understanding of exactly how flooding affects success, so it is difficult to determine the magnitude of the threat posed by sea-level rise. We tested whether variables associated with the timing of nest initiation, tide height, and flooding frequency can be used to estimate three aspects of nest fate: the probability of nest success, the probability of nest failure due to flooding, and the number of offspring lost to flooding. Of the 191 nests that we monitored, only 15% were never flooded and 18% were successful; the mean (± SD) number of flooding events observed per nest was 2.8 ± 2.1 (range: 0–10). The top-performing model for each measure of nest fate included variables related to tidal metrics, but model composition for the three measures differed in the importance of particular tide variables. Both tide height and flooding frequency emerged as important drivers of nest fate in this system. Saltmarsh Sparrow nests appear to be extremely vulnerable to even slight increases in sea level.