In 2018, Fisheries and Oceans Canada initiated the Multidisciplinary Arctic Program (MAP) – Last Ice, the first ecosystem study of the poorly characterized region of the Lincoln Sea in the Marine Protected Area of Tuvaijuittuq, where multiyear ice still resides in the Arctic Ocean. MAP-Last Ice takes a coordinated approach to integrate the physical, biochemical, and ecological components of the sea ice-ocean connected ecosystem and its response to climate and ocean forcings. The cross-disciplinary program establishes baseline ecological knowledge for Tuvaijuittuq and, in particular, for its unique multiyear ice ecosystem. The database provides baseline data on the abundance of bacteria and viruses in multi- and first-year ice and in surface waters of the Lincoln Sea in Tuvaijuittuq, and their relation to bio-physical conditions. The data were collected during the 2018 spring field campaign of the MAP-Last Ice Program, at an ice camp offshore of Canadian Forces Station (CFS) Alert.