The paper analyses the impact of: 1) CO2 pricing; 2) using biodiesel on the multimodal freight transport system in and through the Netherlands taking the changes in the transport demands for road, rail, and inland waterway into account. Special attention is given to the impact on the market share of various barge classes in inland waterway transport. This paper presents the GIS‐based multimodal flow estimation model which is applied in the scenario analysis to simulate, visualise, and evaluate the impacts of the tested policies. The scenario analysis shows that the impact of CO2 pricing is limited in terms of both reducing CO2 emissions and realising modal shift. Pricing CO2 at €90 per ton or using biodiesel B30 (a blend of 30% biofuel and 70% diesel) would achieve similar effects on the total transport network cost increase and modal shift from road to intermodal transport. The analysis shows also that the largest class of barge (VIb) would be less cost efficient than class Va barges if the fuel costs increased by 50%, because the benefit gained by Va barges from less fuel consumption per TEU per km would be higher than the cost saving per TEU per km gained by VIb barges from the scale economy of barge size.