A hydrologic water balance model is implemented to study the dynamics of the complex “Cienaga Grande de Santa Marta” (CGSM) Lagoon. The model simulates the time evolution (half-hourly) of water levels and salinities in 23 water bodies, during several years. The topological relations between the channels and lagoons were constructed with data obtained through field campaigns regarding channel flows, bathymetries and satellite images. To study the interaction between the Caribbean Sea and the CGSM Lagoon, constituent harmonics of the tidal wave were established, and a description of the morphologic behavior of the connection between systems in “La Boca de la Barra” was made. Interannual hydrologic variability is studied with correlations between river discharges in the region and macro-climatic phenomena such as El Nino-Southem Oscillation (ENSO), represented by the Southern Oscillation Index (SOI), and the Sea Surface Temperature on the Pacific Ocean. The results of the water balance model are presented as time series of water levels and salinities for period 1971 - 2000, and for different operational scenarios of the floodgates hydraulic system installed in the Aguas Negras and Renegado channels, for period 1998 - 2000. The model results supports its usage as a decision support system for planning and management of the CGSM lagoon.