Trace metal contamination is ubiquitous around the world and may affect the health of wildlife. Divalent trace metals, including ions of mercury (Hg) and lead (Pb), have been shown to be immunotoxic to avian species. However, little is known about the immunomodulatory effects of trace metal exposure on viral infections, especially in young birds, who may be more sensitive. Therefore, the objective of the current study is to provide more insights in the causality between trace metal exposure and the effects of exposure on the immune responses in young waterfowls. Pekin duckling was used as an animal model to investigate the effects of inorganic divalent Hg (II) and Pb (II) on avian immune responses upon a viral-like challenge with double-stranded RNA. Our results indicate that Hg (II) altered the immune gene expression 24 h post-challenge, as reflected by induction of pro-inflammatory genes IL-8, iNOS, TLR3 and TLR7, and a significant decrease of microRNA-155. Ducklings exposed to Pb (II) showed lower levels of natural antibodies, reduced white blood cell counts and lower heterophil proportions 24 h post-challenge. Although inorganic divalent Hg (II) and Pb (II) showed specific differential effects on the immune response of Pekin ducklings, the overall adverse immunomodulatory outcomes in both cases point to inflammation, impaired B-cell function, and weaker immunocompetence.