The membrane bioreactor (MBR) at the Traverse City Regional Wastewater Treatment Plant (TCRWWTP) has experienced sudden and unpredictable periods of substantial permeability decline since 2011. Early observations detected irregularly-shaped gram-positive bacteria that correlated with plant upsets. Use of biomolecular techniques, such as DNA sequencing of laboratory isolates and the mixed liquor microbial community, and fluorescent in situ hybridization, identified the dispersed organisms as members of the genus Staphylococcus. However, Staphylococcus members were consistently present during normal operation and therefore more likely an indicator of the upset, not the cause. The results suggest that these microorganisms are responding to specific influent wastewater constituents. We chemically analysed seven mixed liquor samples from periods of permeability decline in 2017 and 2018, and four samples from a period of normal operation. During upset conditions, the total carbohydrate content exceeded that of normal operation by 40%. Additionally, mixed liquor calcium concentrations were 65% above normal during the upset in 2017. It is hypothesized and supported through multivariate statistical analysis and estimation of specific resistance to filtration (SRF) values, that a calcium-intermediated polymer bridging mechanism with EPS constituents is one major contributor to fouling and permeability disruptions in the Traverse City MBR.