Water deer (Hydropotes inermis) are among the most common wildlife to approach farmhouses and livestock barns in Korea. We collected 305 water deer from Gangwon (n = 168), South Chungcheong (n = 89), and Gyeongsang (n = 48) provinces in 2010–12 and used PCR and serologic tests to screen the deer for pathogens. In 2010, tests for bovine viral diarrhea virus (BVDV), rotavirus, and Brucella abortus were positive in 8% (5/60), 2% (1/60), and 59% (33/56) of the animals, respectively. In 2010, the water deer were negative for foot-and-mouth disease virus, coronaviruses, and Mycobacterium bovis. All samples collected in 2011 and 2012 were negative for all pathogens analyzed. These results suggest that at least two of the investigated pathogens, BVDV and B. abortus, circulate among water deer in South Korea.