Background: The comprehensive approach to diseases in broad ecological contexts appears as a new challenge for global health and draws on baseline studies to detect changes in the occurrence of pathogens over time. Marsh deer (Blastocerus dichotomus) mortality episodes were described in Argentina and several pathogens associated with environmental and eco-epidemiological factors were indicated as risk factors. To date, the lack of basic health information on these populations has hampered interpretation of findings. This study aimed to provide baseline data on health parameters in marsh deer populations from Argentina. Results: Between May 2014 and December 2016 we determined health parameters in 44 marsh deer with different body condition scores, and studied the pathological lesions in dead animals. Marsh deer with poor body condition had a high burden of the ticks Amblyomma triste and Rhipicephalus microplus. Vector borne agents (VBAs), such as Theileria cervi. Trypanosoma theileri, Trypanosoma evansi, Ehrlichia chaffeensis, Anaplasma platys, Anaplasma odocoilei, Anaplasma marginale, and Candidatus Anaplasma boolense were also found. Haemonchus spp, Ostertagia spp., Trichostrongylus spp. showed the highest infection prevalence. A Multiple Correspondence Analysis suggested a possible association of i) lower body score condition with high tick loads and infection with VBAs and, ii) the impoverished body score with high loads of nemathelminths and well-known harmful gastrointestinal parasites. Conclusions: Our results contribute with knowledge on the life history and health aspects of marsh deer in the study areas. We provide data on the prevalent infectious and parasitic agents in their populations. A range of haematology and serum chemistryvalues, and the occurrence of Fasciola hepatica and Leptospira interrogans serovar pyrogenes were reported for the first time in wild marsh deer from Argentina. The histopathological findings in succumbed animals allowed us to recognize injuries associated or not with their body condition. Our results are the first step in the creation of a baseline on marsh deer health in Argentina. In the future, these data added to new contributions could help improve the interpretation of the findings during mortality events.