Human interventions have a great potential of spatially cornering and limiting species, therefore investigating the species distribution is one of the most crucial issues for managing wildlife populations and suggesting robust conservation strategies. Water deer (Hydropotes inermis) are widespread in China throughout history and are endemic to East Asia. However, they disappeared from Northeast China for years. We rediscovered the water deer in a previous study in Jilin Province, China. Then, we conducted further research in Northeast China to determine their distribution status, supplying fundamental data for the recovery and expansion of their population. An interview survey, line transect survey and infrared camera monitoring were carried out in some counties/cities in Northeast China from June to December 2021. The results showed that the water deer were distributed in Wuchang city of Heilongjiang Province, Changbai Korean Autonomous County, Baishan Municipal District, Ji’an city, Hunchun city, Huadian city, Antu County and Helong County of Jilin Province, Benxi Manchu Autonomous County, Huanren Manchu Autonomous County, Kuandian Manchu Autonomous County, Fengcheng city and Donggang city of Liaoning Province. The ensemble species distribution model constructed by sdm within the TSS of various models that were set as weight revealed that the potential distribution area of the water deer in the study area was 8764.66 km2 (28.77% of the study area). Combining recent studies concerning the distribution of water deer and the current study, we updated the distribution of wild water deer in Northeast China, which is vital for their conservation worldwide.