Currently, the most rapid increase in near-surface air temperature takes place in the Arctic, accompanied by reduced sea ice concentration. Under the resulting retreat of sea ice, the underwater shortwave radiation and, thus, the amount and types of phytoplankton may change. In this study, we use a coupled sea-ice – ocean – ecological model (Darwin-MITgcm) to simulate the variability of the ocean’s major optically active constituents, comprising six phytoplankton functional types (PFTs) and colored dissolved organic matter (CDOM), in response to Arctic amplification. We further set up the general circulation model to account for the biogeochemical processes, in terms of light attenuation, so that their feedback on Arctic Ocean’s physical and biogeochemical properties can be assessed. Here, for the first time, CDOM is included in the underwater light attenuation scheme as a prognostic model variable that interacts with the changes induced by its presence. The coupled model simulation, allowing to consider explicitly the optical constituents, is compared with a constant attenuation depth formulation corresponding to Jerlov water type I, which is the case in most ocean models. Our findings suggest that the presence of CDOM and phytoplankton, by modulating the vertical distribution of the incoming light, affects significantly the upper ocean thermal structure. The promotion of heat-trapping near the surface results in summertime warming, locally even in more than 1°C, and to sea ice reduction. These changes have implications to upper ocean stratification and are accompanied by changes in nutrients supply, as well as in total but also partial PFTs chlorophyll-a.