Biological wastewater treatment is driven by complex interactions between prokaryotes and eukaryotes. Occasionally, filamentous bacteria species, first and foremost Ca. Microthrix parvicella, increase in abundance and lead to detrimental wastewater sludge bulking or floating, causing environmental harm and financial losses. Current mitigation strategies rely heavily on nonspecific chemical interventions, which present environmental risks and lack prolonged effectiveness. Here, we utilise long-term monitoring data from four German wastewater treatment plants (WWTPs) to explore sustainable biocontrol alternatives. Our findings reveal Lotka-Volterra dynamics between Ca. Microthrix parvicella and the protist Arcella spp. Visual and experimental validation demonstrate the suppression of filamentous bacterial growth by predation. We further model these interactions, predicting the biocontrol potential of Arcella spp. for both immediate and sustained efficacy in managing sludge bulking. These results highlight the potential of protists as biological control agents, providing a more sustainable and environmentally friendly alternative to chemical treatment.