In the planning of the tunnel support system, besides the detailed investigation of the geological-geotechnical conditions, it is also important to investigate the structure-tunnel interaction. Especially the structures located in the close vicinity of the tunnels built in unpredictable geological conditions should be considered as a part of the tunnel support system design and the planning should be performed. However, the strong heterogeneity and anisotropy characteristics of karstic environments affect the planning. In this study, a single-track railway tunnel excavated in a relatively thin-bedded, karstic limestone in the Gebze Köseköy Railway project is investigated in terms of structure-tunnel interaction and the importance of grouting. The fact that the tunnel, located in the center of the two piers of the Osmangazi Suspension Bridge approach viaducts, built on the Gulf of Izmit, passes through a shallow overburden, is also an important difficulty in the design of the tunnel. Some karstic caves are determined in the limestones besides its heavily fractured nature. It is concluded that there is a possibility of damage to the bridge as a result of different settlements under the viaduct piers during the tunnel construction with the support to be performed only through the tunnel, and the karstic caves should be filled in order to prevent possible damages. The karstic limestones along the tunnel route are strengthened from the surface by injection of a mixture of water, cement, bentonite, and sand. The interaction of the tunnel with the viaduct after injection is investigated with 2D and 3D numerical analysis and tunnel excavation and support works are started. With the tunnel construction, measurements taken from inside the tunnel and from the viaduct piers, values very close to the predicted deformation limits were obtained by 3D numerical analysis, and the tunnel construction is successfully completed. Despite the extremely difficult conditions, the main reason why no problems are encountered during the tunnel construction is considered to be the grouting.