Bald Eagles (Haliaeetus leucocephalus) and Common Loons (Gavia immer) have been the subject of intensive recovery efforts over 4 decades in New Hampshire. In the last 2 decades, eagles have increased from 1 to 40 territorial pairs, and loons have increased from 208 to 284 territorial pairs. Eagle predation of loons and loon eggs has been documented in a limited but increasing number of cases. We looked for evidence that this predation has begun to limit loon productivity or provoke territorial shifts to avoid predation during the initial period of Bald Eagle population recovery (1998–2013). Using 16 yr of breeding census data, we found support for the prediction that eagle nest proximity may be contributing to >3% of observed loon nest failures. Our findings indicate that eagles may already be exerting a measurable predation pressure. However, at current eagle densities, this pressure does not explain observed local declines in loon abundance. Our counterfactual analysis identified subsets of the data (e.g., loon nest sites on islands) where eagle nest density had the strongest negative association with loon productivity; it may be a useful tool for similar ecological models.