This paper presents a multi-objective optimization model for integrating different transportation modes in the design and operation of an intermodal transportation network in a geographical region. The problem is formulated as a mixed-integer optimization problem that accounts for time and congestion dependent vehicle speeds. We present modeling approach, data analysis and outline the important characteristics of the mathematical programming problem for minimization of transportation cost and time simultaneously. The proposed approach is illustrated on a real-world case using data from Marmara region where approximately 50% industrial goods and services in Turkey are produced.