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Kuwait’s wastewater treatment plants experience severe sludge bulking and foaming problems during the winter months. In an effort to identify the possible causes of these problems, sample of wastewater and sludge was collected from Um-Al-Haiman and Riqqa activated sludge systems each week for 32 weeks. The quality of wastewater was determined following standard methods of water analysis, while the dominant filamentous bacteria were identified and quantified using a molecular method called Vermicon Identification Technology (VIT). Multivariate statistical analysis (namely, Pearson’s correlation analysis and principal component analysis) was then carried out on the obtained datasets of results. Pearson’s correlation analysis revealed several significant associations between filamentous bacteria growth and influent quality and operational modes for the systems. The principal component analysis revealed six components that accounted for more than 70% of the total datasets’ information. The techniques used in this study can also be used to assess the relationship between filamentous bacteria growth and the operating conditions of other activated sludge systems.