International shipping in the Arctic region is one of the key contributors to changes in the region due to the generated air emissions from marine fuels combustion, usage of forest-based biofuels as an alternative to conventional fossil fuels in marine shipping seem as an attractive alternative. However, a system analysis perspective is needed to ensure its sustainability. Life cycle assessment was used to estimate the environmental impacts of the production and use of two forest-based biofuels. These fuels, biodiesel and bioethanol, were derived from pulp and paper mills for use by marine shipping. They were compared to fossil fuels currently used by the marine shipping industry, those being Marine Gas Oil (MGO) and Heavy Fuel Oil (HFO). Future projection scenarios in 2030 and 2050 for estimating the environmental impacts of a transition from fossil fuels to biofuels in Arctic shipping were studied as well. The results indicate that a holistic view is very important for biofuel use. The production and use of forest-based bioethanol (BE) had a significantly lower impact on climate change (CC) potential, but had a higher impact on Human toxicity non-cancer effects (HTX), Human toxicity cancer effects (CE), Particulate matter (PM), Photochemical ozone formation (POF), Acidification potential (AP), Terrestrial eutrophication (TE), Freshwater Eutrophication (FE), Marine eutrophication (ME) and Freshwater Ecotoxicity (FEC). Replacing HFO with forest-based biodiesel reduced the potential AP by 55%. It also had a lower impact on the categories CC, PM, POF, TE, ME and FEC. Furthermore, a reduction in emissions generated by shipping in the Arctic and a better overall environmental performance can be achieved by using blends of MGO with BE.