Water mites were sampled from 15 tributary streams of Mangde Chhu river in Zhemgang and Trongsa districts, Central Bhutan in pre-monsoon (April–May) and post-monsoon (October–November) of 2021. A total of 802 individuals were collected belonging to seven families and 15 genera. The accumulation curve suggests that the sampling efforts were adequate to give a proper overview of genera composition for elevations 500–2,700 m. Eleven genera—Aturus, Kongsbergia, Woolastookia, Atractides, Hygrobates, Lebertia, Piona, Sperchonopsis, Monatractides, Pseudotorrenticola and Testudacarus—and five families—Aturidae, Hygrobatidae, Lebertiidae, Pionidae, and Protziinae—are new records for Bhutan. Independent sample t-tests of genera richness (t, (26) = 0.244, p = 0.809); genera evenness (t, (26) = 0.735, p = 0.469); Shannon diversity index (t, (26) = 0.315, p = 0.755) and dominance (t, (26) = -0.335, p = 0.741) showed no significant differences between pre- and post-monsoon assemblages. Species abundance was also not significantly different (t, (28) = -0.976, p = 0.330). Principal component analysis indicated that the diversity of water mites is negatively associated with several environmental variables including chloride (r = -0.617), ammonia (r = -0.603), magnesium hardness (r = -0.649), total hardness (r = -0.509), temperature (r = -0.556), salinity (r = -0.553), total dissolved solids (r = -0.509) and electrical conductivity (r = -0.464). Diversity was positively correlated with altitude, mainly caused by the higher Palaearctic genera diversity. Similarly, Pearson’s correlation test showed that there was significant negative correlation between mite abundance and the water physio-chemical parameters salinity (r = -0.574, p = 0.032), electrical conductivity (r = -0.536, p = 0.048), total dissolved solids (r = -0.534, p = 0.049), total hardness (r = -0.621, p = 0.018), and chloride concentration (r = -0.545, p = 0.036), indicating sensitivity of water mites to pollution.