In this study, the effect of two different projects on the capacity of a commuter rail line is explored. The study reviews line capacities in the case of a mixed operating system or in the case of operation of commuter trains only. Commuter rail lines operated in two regions of Istanbul are taken as an example. These quite inefficient lines will be modernized and joined and integrated. Two projects exist for updating and integrating these lines, one of which is the Marmaray project. Under the ongoing Marmaray project planned for completion in 2010, the Bosporus will be crossed through a tube that will join the commuter rail lines in the neighboring continents. Another planning alternative, in addition to the Marmaray project, is to build a suspended bridge to serve railway traffic and to allocate this line to high-speed trains and other long-distance trains. This will enable operation of commuter trains and high-speed trains on separate lines. Commuter rail line capacities for both modes of operation are calculated separately using line data and the results are reviewed.