We present the results of species distribution modeling conducted on macrobenthic occurrence data collected between 2002 and 2014 in Arctic fjord – Hornsund. We focus on species from Mollusca and Crustacea taxa. This study investigates the importance of individual environmental factors for benthic species distribution, with a special emphasis on bottom water temperature. It aims to verify the hypothesis that the distribution of species is controlled by low water temperatures in the fjord and that the inner basins of the fjord serve as potential refugia for Arctic species threatened by the climate change-related intensification of warmer water inflows. Our results confirm the importance of bottom water temperature in regulating the presence of benthic fauna in the Hornsund fjord. The distribution of studied species is clearly related to specific water mass – colder (<1°C) or warmer (>1°C); and the preferred temperature regimes seem to be species specific and unrelated to analyzed groups. This study supports the notion that inner basins of the Hornsund fjord are potential refugia for cold water Arctic fauna, while the outer and central basins provide suitable habitats for fauna that prefer warmer waters.