The San Juan Islands Pelagic Ecosystems Function (PEF) marine dataset has been compiled as part of a field-intensive apprenticeship class taught at Friday Harbor Labs during fall quarter, initiated by Jan Newton (UW) and Breck Tyler (UW/FHL) in 2004. More recently, Israel Marquez (UW/FHL) and Becca Guenther (UW/FHL) are leading the oceanographic and marine bird and mammal portions. The dataset time period is from 2004 to the present (files updated annually). Data have been primarily collected from late September to late November, though some spring and summer data exist for some of the years. Oceanographic observations have been carried out at multiple stations in and around the San Juan Channel, but primarily at station N and station S, which have been occupied annually. The oceanographic dataset is composed of four different categories: 1) CTD, 2) Discrete bottle samples, 3) Phytoplankton, and 4) Zooplankton. The marine bird and mammal data are collected on a transect between stations N and S.