The Antarctic sea ice, which undergoes annual freezing and melting, plays a significant role in the global climate cycle. Adverse environmental conditions in the Southern Ocean influence the extent and amount of ice in the Marginal Ice Zones (MIZ), the BioGeoChemical (BGC) cycles, and their interconnected relationships. The ’Pancake’ floes are a composition of porous sea ice matrix with interstitial brine, nutrients, and biological communities inside the pores. To realistically model these multi-phasic and multi-component coupled processes, the extended Theory of Porous Media (eTPM) is used to develop models capable of simulating the different seasonal variations. All critical variables like salinity, ice volume fraction, and temperature, among others, are considered and have their equations of state. The phase transition phenomenon is approached through a micro-macro linking scheme. A Phase- field solidification model coupled with salinity is used to model the micro-scale freezing processes and up-scaled to the macro scale eTPM model. This allows for modeling the salt trapped inside the pores. For the biological part, a BGC flux model for sea ice is also set up to simulate the algal species present in the sea ice matrix. Processes like photosynthesis are dependent on temperature and salinity, and are derived through an ODE-PDE coupling with the eTPM model. Academic simulations and results are presented as validation for the mathematical model. These high-fidelity models will eventually lead to their incorporation into large-scale global climate models.