We report an integrated analysis of new geological and geophysical data from the Lena River delta region to clarify the structural relationships between the Siberian Craton, the Verkhoyansk fold-and-thrust belt, and the Laptev Sea rift system. New geophysical data include the local seismic monitoring (613 earthquakes for the period of 20182024) and the magnetotelluric sounding measurements (MTS, 21 points). A joint interpretation of morphostructural studies, seismic tomography, MTS data, and gravity anomalies leads to the following conclusions. Seismic activity is confined to crustal structures of the Verkhoyansk fold-and-thrust belt and the South Laptev rift but has migrating character within this area. Seismic tomography reveals a two-layer crustal structure on the southwestern side of the study area. The upper layer, characterized by higher vP/vS ratio, corresponds to the structures of the Verkhoyansk fold-and-thrust belt overthrust onto the margin of the Siberian Craton, which are overlain by structures of the South Laptev rift. The top of the lower layer, with a lower vP/vS ratio, dips from southwest to northeast to depths of 1520яkm. This layer corresponds to the Precambrian crystalline basement of the Siberian Craton. This two-layer crustal model is traced beneath the deltaic sediments of the Lena River for approximately 30яkm to the northeast. Further it converts into a single-layer structure with high vP/vS values. MTS data provide detailed information on the upper crustal structure, consistent with the presence of the South Laptev rift between the Bulkur and Bykov faults, as well as with the presence of the Tumat horst to the northeast of the Bykov fault. Modern fault activity is identified by subvertical low-resistivity anomalies from MTS data (fluid-saturated zones) and zones of earthquake hypocenter concentration from seismological data, as observed for the Bulkur, Nizhne-Lena, Bykov, and Sardakh faults.