Empirical orthogonal function (EOF) analyses were performed on 36 coastal zone color scanner (CZCS) images of the Mid-Atlantic Bight and Gulf of Maine taken from February 28, 1979, through July 9, 1979. The EOF procedure was modified to allow images with significant portions of data missing because of clouds to be included in the analysis. Analyses performed both with the temporal and with the spatial means removed from the data produced similar results. A strong gradient existed in the temporal mean from high pigment concentrations nearshore to much lower pigment concentrations offshore. The first mode of the temporally averaged analysis explained 21.5% of the variance and showed a south-to-north pattern corresponding to an April Mid-Atlantic Bight bloom and a June bloom over Nantucket Shoals and Platts Bank. The second temporally averaged mode explained 18.3% of the variance and corresponded to a shelf-wide phytoplankton bloom that resulted in increased pigment concentrations through the spring. The first mode of the spatially averaged analysis explained 59.1% of the variance and had a pattern similar to the temporal mean. The second mode explained an additional 13.2% of the variance and was almost identical to the first mode in the temporally averaged analysis. The inclusion of cloud-containing images introduced some small-scale spatial noise into the EOF analyses. However, the inclusion of these images in the EOF analysis allowed postanalysis image reconstruction that provided estimates of pigment concentrations beneath the clouds. ¿ American Geophysical Union 1989