The harbor seal population in Glacier Bay National Park, Alaska, has declined by over 70% since 1992. The reasons for this decline are not known. We examined serum antibodies and feces for evidence of exposure to multiple pathogens in this population. We also studied harbor seals from a reference site on Kodiak Island. In 2007, we found antibodies against Leptospira spp. in 31% of specimens from harbor seals in Glacier Bay, but no detectable serum antibodies in samples from Kodiak. In 2008, no samples had detectable antibodies against Leptospira spp. No serum antibodies against Toxoplasma gondii, morbilliviruses, or presence of Cryptosporidium in fecal samples were detected. However, Giardia was found in 6% of the fecal samples from Glacier Bay. Our results indicate that the harbor seal population in Glacier Bay National Park could be immunologically naïve to distemper viruses and therefore vulnerable to these pathogens. Given the relatively low prevalence of antibodies and low titers, pathogens likely are not the reason for the harbor seal decline in Glacier Bay.