These data originate from a dissolved organic matter (DOM) degradation experiment carried out at Bylot Island (Qarlikturvik Valley, 73°09’N, 79°58’W), in the eastern Canadian Arctic. The site is a thick peaty terrain underlain with continuous syngenetic permafrost and structured in ice-wedge polygons. It is covered with thousands of shallow ponds forming a typical polygonal tundra landscape. Water was sampled from 6 thermokarst ponds and a 14-day incubation was carried out between 3rd and 16th July 2017 at the water surface. Water was filtered and distributed into bottles exposed to sunlight or covered from it to generate treatments and evaluate the efficiency of DOM photodegradation and biodegradation. Dissolved organic carbon, along with optical variables characterizing the chromophoric fraction of DOM (a320, SUVA254, fluorescent PARAFAC components…) and microbial abundance, were measured at the beginning and end of the incubation. The originality of the study is that ponds were selected to obtain a gradient of terrestrial inputs from surrounding eroding permafrost soil, including two erosive ice-wedge trough ponds, two stable ice-wedge trough ponds and two coalescent polygon ponds.