Smelting activities at Giant Mine (Yellowknife, NWT, Canada) have resulted in high sulfate and arsenic concentrations in nearby lakes. Here we tested whether historic smelting affects current mercury (Hg) cycling in 35 freshwater lakes over a 2800 km² area around the former gold mine. We sampled lake water and sediment over three consecutive years (2015–2017) using a factorial sampling design that accounted for different environmental variables known to affect the net methylmercury (MeHg) levels in water. Stable Hg(II) and MeHg isotope tracers were used to quantify Hg methylation and demethylation rate constants in sediments, and 16S rRNA gene amplicon sequencing was used to characterize microbial community structure. This study reveals that the fraction of methylated total Hg (% MeHg) found in surface water is positively correlated to the sulfate gradient, while the rate at which Hg is methylated (K_m) in sediments is negatively correlated with total arsenic, and positively correlated with dissolved organic carbon, total phosphorous, and % MeHg in the water. Furthermore, 6 of the 28 lakes that had detectable demethylation rate constants (K_d) also had significantly lower DOC concentrations than lakes with non-detectable K_d. Our results also show that legacy pollution from smelting activities is affecting the structure of microbial communities in lake sediments. This study reveals the complex dynamics of Hg cycling in this northern environment, highlighting the importance of large-scale studies in which the effect of multiple pollution gradients (e.g. arsenic and sulfate) must be taken into consideration.