Transformation and distribution of mercury (Hg) species play an important role in the biogeochemical cycling of mercury in aquatic systems. Measurements of water/air exchange fluxes of Hg, reactive mercury (RHg), and dissolved gaseous mercury (DGM) concentrations were conducted at 14 sites in five reservoirs on the Wujiang River, Guizhou, Southwest China. Clear spatial and temporal variations in Hg fluxes, RHg, and DGM concentrations were observed in the study area. Hg fluxes and RHg concentrations exhibited a consistent diurnal variation in the study area, with maximum fluxes and concentrations during daytime. A typical diurnal trend of DGM with elevated concentration at night was observed in a eutrophic reservoir with elevated bacteria abundance, suggesting a bacteria-induced production of DGM in this reservoir. For other reservoirs, a combination of sunlight-stimulated production and loss via photo-induced oxidation and evaporation regulated the diurnal trends of DGM. Seasonal variations with elevated Hg fluxes and RHg concentrations in warm season were noticeable in the study area, which highlighted the combined effect of interrelationships between Hg species in water and environmental parameters. Hg fluxes exhibited much more significant correlations with RHg and THg concentrations and air temperature compared to DGM concentrations and solar radiation. The measured fluxes were significantly higher than those simulated using the water/air thin film Hg0 gradient model. Aside from the potential limitations of dynamic flux chamber method, this may also suggest the thin film gas exchange model is not capable of predicting water/air Hg flux under low wind speed conditions. Additionally, it is speculated that DGM concentrations might vary significantly in surface waters with depth, and measurements of DGM at a depth of 2–4 cm below the water surface probably underestimated the DGM concentration that should be taken into account in simulations of water/air flux using the thin film gas exchange model. An empirical model of water/air Hg flux was developed, and the simulated fluxes were compared well with measurements. The model yields a mean annual Hg emission of 3.2 ± 1.0 kg in the study area.