Purpose The purpose of this paper is to address the limitations of conventional risk matrix based tools such that both positive and negative connotation of uncertainty could be captured within a unified framework that is capable of modeling the direction and strength of causal relationships across uncertainties and prioritizing project uncertainties as both threats and opportunities. Design/methodology/approach Theoretically grounded in the frameworks of Bayesian belief networks (BBNs) and interpretive structural modeling (ISM), this paper develops a structured process for assessing uncertainties in projects. The proposed process is demonstrated by a real application in the construction industry. Findings Project uncertainties must be prioritized on the basis of their network-wide propagation impact within a network setting of interacting threats and opportunities. Prioritization schemes neglecting interdependencies across project uncertainties might result in selecting sub-optimal strategies. Selection of strategies should focus on both identifying common cause uncertainty triggers and establishing the strength of interdependency between interconnected uncertainties. Originality/value This paper introduces a novel approach that integrates both facets of project uncertainties within a project uncertainty network so that decision makers can prioritize uncertainty factors considering the trade-off between threats and opportunities as well as their interactions. The ISM based development of the network structure helps in identifying common cause uncertainty triggers whereas the modeling of a BBN makes it possible to visualize the propagation impact of uncertainties within a network setting. Further, the proposed approach utilizes risk matrix data for project managers to be able to adopt this approach in practice. The proposed process can be used by practitioners while developing uncertainty management strategies, preparing risk management plans and formulating their contract strategy.