Diatom and silicoflagellate assemblages in cores EW0408-47JC, -47TC, -46MC (57° 34.5278′ N, 136° 3.7764′ W, 114 m water depth) taken from the outer portion of Slocum Arm, a post-glacial fjord in southeastern Alaska, reveal the paleoclimatic and paleoceanographic evolution of the eastern margin of the Gulf of Alaska (GoA) during the past 10,000 years. Between ~ 10 and 6.8 cal ka, periods of low salinity and cool water conditions alternated with brief intervals marked by the increased influx of oceanic, more saline and likely warmer waters. Increased surface water stability characterized by a middle Holocene interval between ~ 6.8 and 3.2 cal ka is typified by increased abundances of northeastern Pacific Thalassiosira spp. that are indicative of spring coastal blooms and decreased abundances of warm and higher salinity oceanic diatoms. At ~ 3.2 cal ka, an abrupt increase in both the relative contribution of oceanic diatoms and silicoflagellates suggestive of cooler upwelling conditions occurred in the -47JC record. A stepwise increase in alkenone sea surface temperature in northern GoA core EW0408-85JC and increase in southern sourced precipitation in the carbonate δ¹⁸O record of Jellybean Lake (Yukon) present evidence that this ~ 3.2 cal ka event coincided with the onset of enhanced positive Pacific Decadal Oscillation-like (PDO) conditions in the GoA. These positive PDO-like conditions persisted until ~ 1.0 cal ka and were followed by high amplitude fluctuations in the relative abundance of diatom and silicoflagellate assemblages.