Influenza A virus (IAV) infections in shorebirds at Delaware Bay, New Jersey, US, have historically included avian hemagglutinin (HA) subtypes H1–13 and H16. In a given year, infections are characterized by a limited number of HA and neuraminidase subtypes and a dominant HA subtype that often represents >50% of all isolates. Predominant HA subtypes shift between consecutive years. In addition, infection prevalence is consistently higher in Ruddy Turnstones (RUTU; Arenaria interpres morinella) compared to Red Knots (REKN; Calidris canutus rufa), despite comparable rates of exposure. To investigate a potential immunological basis for this phenomenon, a virus microneutralization assay was used to detect subtype-specific, neutralizing antibodies to H1–H12 in sera collected from RUTUs from 2012–16 and REKNs in 2012, 2013, and 2016. Neutralizing antibodies to one or more subtypes were detected in 36% (222/611) of RUTUs. Prevalence of antibodies to subtypes H6 and H11 remained high throughout the study, and these virus subtypes were isolated every year, suggesting a continual source of exposure. Antibody prevalence was intermediate for most IAV subtypes that were isolated in 2–3 of 5 yr (H1, H3, H5, H9, H10, and H12) but was low for H7 viruses, despite the isolation of this virus subtype in 3 of 5 yr. This suggests a reduced antigenicity of H7 IAVs compared to other subtypes. Antibody prevalence was low for H4 virus that was isolated once, and H2 and H8 viruses that were never isolated. Neutralizing antibodies were detected in 66% (169/257) of REKNs and subtype-specific antibody prevalences were higher in REKNs than RUTUs with few exceptions. The results suggest that population immunity influences which species is infected at Delaware Bay, indicate that IAV dynamics are subtype-dependent, and demonstrate the utility of the microneutralization assay as a supportive tool for field research.