There are increasing concerns about potential neurotoxicity of chronic methylmercury (MeHg) exposure in Arctic wildlife and human populations. The relationships between mercury (Hg), MeHg, inorganic Hg (iHg), and selenium (Se) exposure, and neurochemical and molecular biomarkers in beluga whales (Delphinapterus leucas (Pallas, 1776)) were characterized. Samples were collected in 2008 (n = 20) and 2010 (n = 15) in the Canadian Arctic from hunter-harvested beluga whales. Total Hg concentrations in the temporal cortex and cerebellum were 21.0 ± 22.6 mg kg −1 dry weight (dw) and 14.9 ± 18.9 mg kg −1 dw, respectively. Monoamine oxidase (MAO) activity was predicted by MeHg and the molar ratio of total Hg to Se (Hg:Se, p < 0.05); MAO-A mRNA transcription levels were predicted by iHg and Se (p < 0.05). Muscarinic AChR binding was predicted by MeHg (p < 0.05) and Hg:Se molar ratio (p < 0.05), and mRNA transcription levels of mAChR m1 was predicted by the Hg:Se molar ratio (p < 0.05). These results suggest that the cholinergic and dopaminergic signaling pathway in Eastern Beaufort Sea beluga whales may be sensitive to MeHg exposure. The response of beluga whales to MeHg exposure at a physiological and population level remains to be elucidated.