We present geochemical and hydrochemical information on individual permafrost and seawater samples from the Yukon Coast in the western Canadian Arctic used for an incubation experiment. The experiment mimicked erosion of permafrost coasts in the Arctic by mixing different kind of permafrost (i.e. organic-enriched and mineral) with ambient seawater at temperatures of 4 and 16°C during the course of 4 months (the approximate length of an Arctic open-water season). The data sets contain information on basic geochemical parameters measured before and after the experiment and on the production of greenhouse gases, which include carbon dioxide (CO2) and methane (CH4). This data set contains the geochemical and hydrochemical data for permafrost and seawater as well as the total amount of CO2 and CH4 cumulated during the course of the experiment. The study aims at understanding the role of eroding permafrost coasts for the Arctic carbon cycle and budget.