Integrated Waste Management Systems (IWMS) are very complex systems with a lot of uncertainty. These can be defined as the selection and application of suitable techniques, technologies and management programs to achieve waste management objectives and goals. In order to support the decision making process in waste management we propose the use of Fuzzy Cognitive Map (FCM) and Bacterial Evolutionary Algorithm (BEA) methods since the combination of the FCM and BEA seem to be suitable to model complex mechanisms such as IWMS. While the FCM is formed for a chosen system by determining the concepts and their relationships, it is possible to quantitatively simulate the system considering its parameters. However, if the time series of the factors of the system are known, then the connection matrix of FCM, thus the causal relations among the parameters can be determined by optimization. This way a more objective description of IWMS can be given.