Methylmercury (MeHg) readily bioaccumulates and biomagnifies in aquatic food webs leading to elevated concentrations in fish and may thus induce toxicity. Oxidative stress is a suggested effect of MeHg bioaccumulation in fish. However, studies on how MeHg triggers oxidative stress in wild fish are scarce. The purpose of this study was to link the subcellular distribution of MeHg in the liver of northern pike from the St. Maurice River (Québec, Canada), affected by two run-of-river (RoR) dams, artificial wetlands, forest fires, and logging activity, to lipid peroxidation as an indicator of oxidative stress. We also evaluated the protective effects of the glutathione (GSH) system and selenium (Se), as they are known to alleviate MeHg toxicity. A customized subcellular partitioning protocol was used to separate the liver into metal-sensitive (mitochondria, microsome/lysosome and HDP - heat-denatured proteins) and metal-detoxified fractions (metal-rich granules and HSP - heat stable proteins). We examined the relation among THg, MeHg, and Se concentration in livers and subcellular fractions, and the hepatic ratio of total GSH (GSHt) to oxidized glutathione (GSSG) on lipid peroxidation levels, using the concentrations of malondialdehyde (MDA), a product of lipid peroxidation. Results showed that hepatic MDA concentration was positively correlated with the combined MeHg and Se concentration in northern pike liver (r2 = 0.88, p < 0.001) and that MDA concentrations were best predicted only by MeHg associated with the mitochondria (r2 = 0.71, p < 0.001). On the other hand, there was no significant relationship between the MDA concentration and the cellular thiol status, represented as the GSH/GSSG ratio. We also observed a positive significant relationship between MDA concentration and the Se:Hg molar ratio, suggesting that hepatic Se concentration might not be sufficient to confer a protective effect against MeHg induced oxidative stress.