Sustainable wastemanagement systems necessarily include many interacting factors. Due to the complexity and uncertainties occurring in sustainable waste management systems, we propose the use of Fuzzy Cognitive Maps (FCM) and Bacterial Evolutionary Algorithm (BEA) [1] to support the planning and decision making process of integrated systems, as the combination of methods FCM and BEA seems to be suitable to model such complex mechanisms as Integrated Waste Management Systems (IWMS). This paper is an attempt to assess the sustainability of the IWMS in a holistic approach. While the FCM model represents the IWMS as a whole, the BEA is used for parameter optimization and identification. An interpretation of the results obtained by the FCMfor the actual regional IWMS is also presented. We have obtained some surprising results, contradicting the general assumptions in the literature concerning the relative importance of constituting components in waste management systems.