580-km length marine magnetic study was performed at the Northern Marmara Shelf and the Lagoon Küçükçekmece to provide new datasets to understand the submarine structures. The distributions of the relatively complex and differentiated low and high magnetic anomalies indicate that the study area was affected by the multiple tectonic regimes. While the magnetic highs correspond with the folding structures, magnetic low anomalies well match with the lineaments determined from the seismic profiles. Magnetic anomalies support an E-W trending fault, controlling the anticlinorium system and NNE-SSW faults related to the compressional tectonics. These magnetic structures might be associated with Thrace Eskisehir Fault Zone, an older right-lateral strike-slip fault, which was the most dominant tectonic element before the North Anatolian Fault Zone. In addition to three appx, N-S trending faults are defined beneath the Lagoon Küçükçekmece from the total and residual magnetic anomaly grids.