Boreal rivers deliver dissolved organic carbon (DOC), mercury (Hg), and its neurotoxic form, methylmercury (MeHg), from contributing landscapes to downstream waters. In northern regions, thawing permafrost (i.e., perennially frozen ground) in peatland environments may release Hg, MeHg, and DOC from soils to rivers. Over 3 years, we measured the concentrations of water chemistry in two boreal creeks with differing contributing landscapes in the discontinuous permafrost region of the Dehcho (Northwest Territories, Canada). Our results showed different patterns in analyte concentrations versus yields (i.e., annual analyte mass delivered per unit area) between the sites. At the peatland-dominated Scotty Creek, concentrations of MeHg and DOC were consistently high and not primarily controlled by discharge. Still, runoff and analyte yields varied annually as peatlands stored water in a dry year and discharged water in wet years. At Smith Creek, with a mixed landscape of mountains, peatlands, and forests, concentrations of DOC and Hg increased during high-flow events as runoff contributions from peatlands increased. Over the monitoring period, analyte yields at the mixed catchment varied less due to consistent groundwater inputs and runoff generation from steeper slopes. Changing runoff due to climate change and permafrost thaw will likely alter analyte yields in the region.