A coupled numerical model for hydrodynamics and nutrients/oxygen transport inside Ciénaga Grande de Santa Marta lagoon complex (Colombia) was developed using the MOHID Water modelling platform. Preliminary results show coherency with monitoring data for the main lagoon and La Barra strait, both for water level and annual salinity fluctuations. However, further observations inside Pajarales complex are required to achieve an appropriate system-wide hydrodynamic representation. Due to a lack of sufficient information on the coefficients for the nutrient transport processes, the water quality module has only been able to simulate the dynamics between biotic-abiotic factors inside the system for weeklong periods. Therefore, further calibration of the phytoplankton-nitrogen compartment is necessary to perform long-term simulations. Once adjusted, the model will become a powerful tool to assess changes in the system dynamics under diverse intervention scenarios, providing critical support to decision making processes.