Inconnu Stenodus leucichthys is a large, long-lived piscivorous whitefish found in the Arctic and subarctic waters of Alaska. In the Kotzebue region of northwestern Alaska, Inconnu is one of the most important fishes harvested for subsistence purposes. With ongoing climate change, it is important to understand how a changing environment will affect Inconnu habitat use. This study described the habitat use of Inconnu in the Hotham Inlet/Selawik Lake complex from 2010 to 2012. Data collection consisted of surgically implanting acoustic telemetry tags in 80 fish from both rivers in 2010 and 2011 (n = 320), and deploying a fixed array of 20 Vemco VR2W acoustic receiving stations affixed with archival tags throughout the study area. Inconnu were detected at water temperatures and salinities ranging from −1.39 to 23.51 °C and 0 to 31.3 psu, respectively, and there was no detection of stock-specific or temporal trends in habitat use. Fish occupied colder water temperatures (−0.5 to 0.5 °C) during winter and primarily occupied the upper (15 °C) and lower (0 °C) ends of the temperature spectrum during summer. Although Inconnu occupied the entire range of salinities available during summer and winter months, they generally occupied waters of 5 to 20 psu. By providing a more thorough account of Inconnu habitat use, our results contribute baseline data for future comparisons to evaluate effects from climate-induced changes to Inconnu sustainability.