An extensive network of urban and transportation systems is planned within the Abu Dhabi 2030 master plan. This includes planning, implementing and operating underground infrastructure for which it is extremely important to consider the uncertainties, and the inherent risks, affecting them. The research presented here intends to account for natural geological uncertainties affecting underground infrastructure within the Abu Dhabi context through an integrated approach. The study of subsurface information, in areas for which future underground transportation is planned, identified the presence of gypsum within the tertiary bedrock that may be problematic due to its susceptibility to volume change by dissolution or swelling. The paper discusses how an existing a decision support system (Decision Aids for Tunneling, see eg. Einstein, 2004) considers geology- and construction related uncertainties, and then produce cost-, time- and resource distributions. This in turn will serve as a basis for risk analysis and decision making regarding a variety of hazards including gypsum dissolution in Abu Dhabi. Very importantly and as shown, such a comprehensive tool will be integrated with existing optimization tools for transport infrastructure planning (Costa et al., 2013) that relate the planning decisions and the infrastructure layout with the infrastructure performance.