Production of natural gas and crude oil in the eastern regions of Russia was accelerated in the past decade, and both the upstream and midstream segments of the oil and gas industry continue to grow at a fast pace. Innovative solutions are needed for engineering and construction surveys aimed to justify options for choosing routes and methods for laying underwater pipeline sections across large rivers and water reservoirs. In our region, positive experience has been gained by employing modern technologies to optimize routing and reduce the costs of detailed surveys. In the project of the Kovykta – Sayansk – Angarsk – Irkutsk gas pipeline construction, an optimal route across the Bratsk water reservoir was chosen based on the results of several stages of investigation, including continuous seismic profiling and side-scan sonar scanning of the reservoir bed. At the first stage, the mosaic maps of side-scan sonograms and a 3D digital model of the reservoir bed bathymetry were constructed and used to develop and propose three options for the gas pipeline design and its route across the reservoir area. At the second stage, detailed underwater and onshore geophysical and drilling operations were carried out along the proposed routes. Based on the transverse profiles, a decision was taken to lay the pipeline section across the reservoir area in a trench along the northern route, which was justified as an economically and technologically optimal solution. In the winter period when the water reservoir surface was covered with thick ice, the northern route was investigated in detail by drilling and seismic survey operations using vertical seismometer cable assemblies and the inverse travel time curve technique. With reference to the velocity law, the travel time sections were processed and converted into depth profiles. A petrophysical model of bottom sediments was constructed, and a scheme was developed to ensure proper processing and interpreting of seismic and acoustic data. Four structural-material complexes were identified: modern silts; underwater eluvial and alluvial deposits; disintegrated and low-strength bedrocks of the Upper Lena Formation; and unaltered bedrock sandstones and siltstones. The continuous seismic profiles and the data from the vertical seismometer cable assemblies were interpreted, and a neotectonic map of bottom sediments was constructed. By analyzing the fault kinematics, it was revealed that normal faults and reverse faults with low-amplitude horizontal shear dominated in the study area; the mapped faults were mainly rootless structures; and displacements along the faults occurred due to a laminar flow of the Cambrian salt layers. An increase in tectonic activity from north to south was explained by the correspondingly degraded strength properties of the bedrocks. Modern neotectonic structures detected from the survey results gave evidence that that the hydrostatic pressure increased after the reservoir had been filled with water, and the phenomenon of reservoir-related seismicity was observed in the study area. Based on the comprehensive geological and geophysical survey data, the geological and engineering conditions of the proposed construction sites were clarified, and the most appropriate route and design of the gas pipeline section across the reservoir area was approved. This study provided the pipeline designers with the qualitative and quantitative information on the phenomena and factors complicating the conditions for laying the gas pipeline in the study area.