The Hudson Bay complex (HBC) is home to numerous indigenous communities that traditionally have relied heavily on its marine resources. The nutritional quality and stocks of the entire HBC food web depend in large part on the phytoplankton production of bioactive molecules (long chain polyunsaturated fatty acids and carotenoids) and their transfer through trophic levels. The purpose of this study was thus to determine which molecules were produced during spring phytoplankton blooms, as well as the environmental factors driving this production. We investigated 21 stations in 5 sub-regions of the HBC. At the time of sampling, the sub-regions studied had different environmental settings (e.g., ice cover, nutrients, seawater salinity and temperature) conditioning their bloom stages. Pre- and post-bloom stages were associated with relatively low concentrations of bioactive molecules (either fatty acids or carotenoids). In contrast, the highest concentrations of bioactive molecules (dominated by eicosapentaenoic acid and fucoxanthin) were associated with the diatom bloom that typically occurs at the ice edge when silicates remain available. Interestingly, the large riverine inputs in eastern Hudson Bay led to a change in protist composition (larger contribution of Dinophyceae), resulting in lower while more diverse content of bioactive molecules, whether fatty acids (e.g., aa-linolenic acid) or carotenoids (e.g., peridinin). As greater stratification of the HBC is expected in the future, we suggest that a mixotrophic/heterotrophic flagellate-based food web would become more prevalent, resulting in a smaller supply of bioactive molecules for the food web.