The concentration of mercury (Hg) in eggs that causes reduced hatching success is regarded as a critical end point for Hg toxicity in birds. However, incorporating effects of in ovo mercury exposure on chick health and survival could improve risk assessment. We developed equations to predict Hg in eggs using Hg in chick down feathers, and vice versa, by assessing the relationship between Hg in feathers (0.5−32.4 μg g−1 fw) and eggs (0.04−2.79 μg g−1 fww) for three waterbird species in San Francisco Bay, CA. Feather Hg sampled from embryos of pipping eggs was highly correlated with fresh whole-egg Hg (n = 94, r2 = 0.96). Additionally, using an egg microsampling technique, albumen Hg was correlated with feather Hg sampled from chicks in the same nest (n = 28, r2 = 0.79). Down feather Hg in recaptured chicks (≤10 days old) was correlated with down feather Hg at hatching (≤3 days old; n = 88, r2 = 0.74). Our results demonstrate the utility of using down feathers of chicks ≤10 days of age to nonlethally predict Hg in eggs and thus provide the ability to develop exposure thresholds for eggs that incorporate in ovo Hg’s effects on both egg hatchability and subsequent chick mortality.