Recent scientific investigations have revealed the deep structure and fault mechanisms in the Marmara Sea and surroundings. However, magnetic and gravity anomalies display interesting features which were not resolved in detail. In this paper, simple two-dimensional magnetic and gravity models are constructed utilizing parameters such as the density contrast and susceptibilities obtained from a borehole, seismic sections and field susceptibility measurements, respectively. The gravity model shows the existence of horst-like structures, as suggested previously. The top of the magnetic bodies in the Marmara Sea is close to the sea bottom. In general, these magnetic bodies are fault-related. The gravity model complies with the seismic base map, which was constructed previously. The magnetic anomalies of anomalous regions of the Cinarcik and Western Basins demonstrate slight anticlockwise block rotations, while large anticlockwise block rotation is observed in the eastern extremity of the Marmara Sea. Geophysical data and modeling results suggest that the origin and evaluation of the Marmara Sea began with the possibility of emplacement of horst-like structures in the Central Ridge during the Palaeozoic or earlier followed by block rotations and intrusion of the magnetic material into the upper crust with sediment deposition and faulting. It can also be suggested that the horst-like structures in the central Marmara act to diffuse the propagation of the Northern Boundary Fault (NBF). This aspect is correlated with the focal mechanisms of the major earthquakes.