Soft-shell clams, Mya arenaria, a commercially harvested and once economically important species in Maryland's Chesapeake Bay, have experienced a dramatic and persistent population decline since the peak harvests of the 1960s. Many factors have contributed to population decline, including overharvesting, environmental degradation, predation, lack of genetic diversity, and disease. In 2000, the Maryland Department of Natural Resources began an annual disease surveillance program for soft-shell clams. In 2002, intranuclear inclusions were identified within hypertrophied gill epithelia of many clams, but the cause of these lesions was unknown. The principle objectives of this research were to (1) characterize the agent causing gill epithelial nuclear hypertrophy by light and electron microscopy, next-generation sequencing and in situ hybridization; (2) perform a retrospective five year histological health survey to determine the distribution and prevalence of this condition and other diseases, infections or conditions in archived samples of Mya arenaria collected from Maryland's Chesapeake Bay from 2005 to 2009; and (3) perform a metagenomic analysis of viral diversity in Chesapeake Bay soft-shell clams. Light and transmission electron microscopy revealed Feulgen-positive, finely granular, amphophilic, intranuclear inclusions that marginated chromatin, and nonenveloped, moderately electron dense, icosahedral, 75–82 nm virus-like particles that occasionally formed paracrystalline arrays. To assess the overall health of this population, 630 wild soft-shell clams from 18 locations within Maryland's Chesapeake Bay collected from 2005 to 2009 were examined. Intranuclear virus-like inclusions, Perkinsus spp., unidentified pyriform ciliates, trichodinid ciliates, cestodes, copepods, rickettsia-like organisms, bacteria, disseminated neoplasia, a single polyp, renal concretions, hemocytic infiltration and pericardial gland concretions were identified. The virome of three clams was analyzed using next-generation sequencing technology (Illumina Genome Analyzer IIx). Viral families represented included Asfarviridae, Baculoviridae, Caulimovirdae, Circoviridae, Coronaviridae, Herpesviridae, Irodoviridae, Mimiviridae, Myoviridae, Nanoviridae, Nimaviridae, Parvoviridae, Phycodnaviridae, Polydnaviridae, Polyomaviridae, Poxviridae, and Retroviridae. Sequences with identities to numerous unclassified viruses were also present. Phylogenetic analysis of sequences recognized as herpesvirus terminases using BLASTx showed genetic similarity with other molluskan herpesviruses and in situ hybridization using a digoxigenin-labeled DNA probe provided further evidence to support the presence of a novel herpesvirus in soft-shell clams. Results from this study broaden our understanding of pathologic conditions which may be impacting this population and can be used for the management of this species.