The increasing volumes of road transportation contribute to congestion on road, which leads to delays and other negative impacts on the reliability of transportation. Moreover, transportation is one of the main contributors to the growth of carbon dioxide equivalent emissions, where the impact of road transportation is significant. Therefore, governmental organizations and private commercial companies are looking for greener transportation solutions to eliminate the negative externalities of road transportation. In this paper, we present a novel solution framework to support the operational-level decisions for intermodal transportation networks using a combination of an optimization model and simulation. The simulation model includes stochastic elements in form of uncertain travel times, whereas the optimization model represents a deterministic and linear multi-commodity service network design formulation. The intermodal transportation plan can be optimized according to different objectives, including costs, time and CO 2e emissions. The proposed approach is successfully implemented to real-life scenarios where differences in transportation plans for alternative objectives are presented. The solutions for transportation networks with up to 250 services and 20 orders show that the approach is capable of delivering reliable solutions and identifying possible disruptions and alternatives for adapting the unreliable transportation plans.