Mercury contamination in the Florida Everglades has reportedly played a role in the recent decline of wading birds, although no studies have identified a mechanism leading to population-level effects. We assessed feather mercury levels in great egret (Ardea alba; n = 91) and white ibis (Eudocimus albus; n = 46) nestlings at breeding colonies in the Florida Everglades during a year (2006) with excellent breeding conditions (characterized by hydrology leading to concentrated prey) and a year with below average breeding conditions (2007). We also assessed the physiological condition of those nestlings based on levels of plasma and fecal corticosterone metabolites, and stress proteins 60 and 70. Mercury levels were higher in both species during the good breeding condition year (great egret = 6.25 μg/g ± 0.81 SE, white ibis = 1.47 μg/g ± 0.41 SE) and lower in the below average breeding year (great egret = 1.60 μg/g ± 0.11 SE, white ibis = 0.20 μg/g ± 0.03 SE). Nestlings were in better physiological condition in 2006, the year with higher feather mercury levels. These results support the hypothesis that nestlings are protected from the harmful effects of mercury through deposition of mercury in growing feathers. We found evidence to suggest shifts in diets of the two species, as a function of prey availability, thus altering their exposure profiles. However, we found no evidence to suggest they respond differently to mercury exposure