The seismic activity of the middle strand of the North Anatolian Fault (MNAF), Northwestern Turkey, is debated because of its quiescence during the instrumental period, in contrast to a significant historical activity documented by several chronicles over the last two millennia. Here, we focus on Lake Iznik, bordered by the MNAF, to get a new insight into its long-term seismicity and its tectonic setting. The study of lacustrine sediment cores reveals fourteen earthquake-induced turbidites since their ages correspond to seismic events during the past two millennia. Bathymetry and high-resolution seismic reflection data allow describing two hitherto unknown subaquatic active fault structures (the South Boyalica and Iznik faults) that belong to the MNAF system. Sediment cores sampled on both sides of the Iznik Fault document an event deposit and a sedimentary unit vertically offset of ~ 40 cm interpreted as the last rupture during the 1065 CE destructive earthquake. Older events are supposed on this fault more than a thousand years ago. Further studies will help to estimate the horizontal coseismic offset of this oblique-slip fault and the calendar of older ruptures. The current seismic gap of thousand years on this segment greatly increases the seismic hazard in this region and must be considered in the seismic risk assessment of the NAF system.