Global change has dramatically impacted aquaculture in the US. For the Pacific oyster (Crassostrea [Magallana] gigas), disease prevalence and summer heatwaves result in regular mortalities on the US West Coast. High latitude Pacific oyster farms in Alaska may be more resilient to climate change due to cold water temperatures at the lower limit of the oyster’s physiology. However, the environmental dynamics and productivity of this highly seasonal and glacially influenced nearshore region, and the impacts on the Pacific oyster physiology, are poorly understood. This research provides an assessment of the seasonal dynamics of oceanography, phytoplankton communities, and oyster tissue quality over three years of sampling at a Southeast Alaska oyster farm. The results of this study provide a better understanding of nearshore dynamics in the estuarine environment of Southeast Alaska’s inside waters to aid in future site suitability analyses and improve our understanding of Pacific oyster exposure to stressful and beneficial conditions. This region is also prone to spatially and temporally discrete harmful algal blooms (HABs), and the data collected in this study improve our understanding of the conditions that contribute to HAB events.