The data package "Sea Otter Aerial Survey Data from Glacier Bay National Park and Preserve, 1999-2012" provides raw data for examining abundance and distribution of northern sea otters (Enhydra lutris kenyoni) in Glacier Bay National Park and Preserve in southeast Alaska, based on data collected during a series of population-wide aerial surveys. The USGS aerial sea otter surveys have been completed multiple times using consistent methodology involving aerial-based counts. The surveys provide data and a population estimate that Park and other Federal management agencies use for decision making and planning additional research. This data package includes a series of files with the raw digital data that was used for population estimates and population modeling found in related manuscripts.