Marmara Sea (MS) lies in the strategic crossroad, accommodating one of the busiest shipping routes in the world. In general, there is a two-layer current system in the MS and Turkish Straits system; the brackish waters originating in the Black Sea (BS) (18 PSU) moving southward to the Aegean Sea (AS), and a lower layer return flow of saltier Aegean waters (38.5 PSU) back to the BS. This variability poses a challenging task within the modeling perspective. In this research, 3D hydrodynamic modeling of MS is performed in order to investigate the spatial and temporal behavior of elevations between years 2000 and 2015. During the calibration process, the grid configuration, time step, and model coefficients (Manning bed roughness coefficient, a wind drag coefficient and horizontal viscosity are coefficients) are adjusted until the computed solution produced the best match to the observed data such as water surface elevations, velocities, and net discharges. To this end, a series of simulations are made. As a result, the observed and the predicted water surface elevations follow each other very closely. The developed model could accurately estimate the net discharge as well. In order to understand the behavior of MS, elevation pattern is calculated and depicted both on annual and seasonal scales. It is demonstrated that the influence of seasonally varying strong fresh water river discharges of Danube in BS have strong influence on the water mass characteristics of the MS.