ABSTRACT The farming of Pacific oysters ( Crassostrea [Magallana] gigas ) is a rapidly growing industry in Alaska, where farms represent some of the highest latitude oyster cultivation efforts in the world. Little is known about the nearshore oceanography where Alaskan farms are located, or how the subarctic marine context influences oyster tissue quality. This research begins to elucidate those relationships and seasonal variation therein through regular sampling of water column parameters, phytoplankton community composition, and Pacific oyster tissue. Results suggest both benefits and challenges to cultivating Pacific oysters in this dynamic region in Alaska. Benefits included low temperatures that inhibited spawning, resulting in Pacific oysters with year‐round high levels of lipids and polyunsaturated fatty acids. Challenges included a later onset of the spring phytoplankton bloom, resulting in a short growing season compared to other growing regions, occasional blooms of the harmful algal genus Alexandrium spp. that resulted in periods of elevated levels of paralytic shellfish toxins, and intensifying climate variability and ocean acidification. The results of this study provide a better understanding of nearshore dynamics in the estuarine environment of Southeast Alaska's inside waters, which will aid in future site suitability analyses and improve our understanding of cultivating Pacific oysters in this region. As increasingly extreme summer heatwaves contribute to oyster mortality events and other challenges at lower latitude farms, the relatively cold waters at Southeast Alaska oyster farms may offer a buffer against stressors associated with climate variability.