Climate warming in the Arctic is thawing permafrost soils and mobilizing ancient dissolved organic matter (DOM) from deeper soil horizons to surface waters. Once flushed to arctic surface waters, DOM is degraded by sunlight to carbon dioxide (CO2), which can be returned to the atmosphere and positively reinforce climate warming, or to partially oxidized compounds exported to the ocean. Thawing permafrost soils are expected to shift the chemical composition of DOM exported to and photo-degraded in arctic surface waters. However, the molecular controls on DOM photo-degradation remain poorly understood, making it difficult to predict how shifting chemical composition may alter DOM photo-degradation in arctic surface waters. To address this knowledge gap, we quantified the susceptibility of DOM draining the shallow organic mat and the deeper permafrost layer to complete and partial photo-oxidation, and investigated changes in chemical composition of DOM following sunlight exposure. Despite significant differences in initial chemical composition, permafrost and organic mat DOM had similar susceptibilities to photo-mineralization. Concurrent losses of carboxyl moieties and shifts in chemical composition during photo-degradation indicated that carboxyl-rich tannin-like compounds strongly contributed to the CO2 produced when organic mat or permafrost DOM was exposed to sunlight. Permafrost DOM had a higher susceptibility to partial photo-oxidation compared to organic mat DOM, potentially due to a lower abundance of phenolic compounds that act as “antioxidants” and thus slow or inhibit the photo-oxidation of DOM. These results demonstrated how chemical composition controls the complete and partial photo-oxidation of DOM in arctic surface waters, and that DOM photo-degradation will likely remain an important component of the freshwater C budget in the Arctic with increased inputs of permafrost DOM to surface waters.