Since 1987, seabirds and marine mammals have been surveyed along the CalCOFI transect during daylight hours while the ship is underway. Data counts on seabirds and marine mammals are entered into a handheld computer in real time and are available to filter or download on the Datazoo webpage. Bird observers participating on CalCOFI cruises are provided by support from the Farallon Institute for Advanced Ecosystem Research (Jul 2007 to present) and Point Reyes Bird Observatory (PRBO, 1987-2006).

Sea birds are counted within a 300-meter wide strip off to one side of the ship. Counts were made while underway between stations during periods of daylight. These counts were summed over 20 nautical mile (nm) intervals, or the distance between consecutive stations, whichever was less. Included at the end of each data report are individual maps of the most numerous bird species (individuals/NM).