The coupled physical–biogeochemical dynamics of the Baltic Sea are challenging to simulate due to its complex bathymetry, strong stratification, and high optical turbidity. This study evaluates a multi-source data assimilation framework using a three-dimensional coupled model, comparing univariable (chlorophyll‑a only) and multivariable (chlorophyll‑a plus sea surface temperature) assimilation strategies. Our results quantify the vertical and dynamical limits of surface-constrained assimilation in stratified marginal seas. Satellite chlorophyll‑a assimilation markedly improves the spatial and seasonal representation of surface phytoplankton biomass, but in situ profiles are necessary to accurately reconstruct the subsurface chlorophyll maximum. Physical and biological constraints are complementary, and their joint assimilation yields a synergistic improvement, substantially reducing thermohaline biases and enhancing overall model consistency. Although chlorophyll‑a increases can modify subsurface heating through bio‑optical feedback, deep‑water oxygen profiles at monitoring stations remain insensitive to surface‑focused constraints and are governed instead by physical ventilation and remineralization. Crucially, the joint configuration provides a cross‑variable regularization that prevents noisy biological updates from degrading the physical state. These results demonstrate that, in optically complex marginal seas, joint physical–biogeochemical assimilation is essential to overcome the limitations of univariable frameworks and to ensure that surface observations translate into an accurate representation of the full water column.