Membrane-based biofilm reactors for wastewater treatment will play a pivotal role in the next generation of sustainable wastewater treatment and water reuse systems. Countless studies have been conducted regarding both scaling up the reactor systems and managing and understanding the complex biofilm communities present in the reactors. However, the conclusions drawn are weakened by the fact that protozoan predation is largely ignored, despite their ubiquitous presence in biofilm systems. This may result in misleading assessments of results and failures in system control.This dissertation explores the impacts and control of predation on biofilms in membrane-based wastewater treatment processes. Three representative types of biofilm systems were studied: (1) a heterotrophic membrane-aerated biofilm reactor (MABR), (2) a nitrifying MABR, (3) a membrane-based biofilm photobioreactor (MBPR), and (4) a novel biofilm reactor that allows for control of protozoan predation. During the first three studies, conditions both with the presence of protozoa and with the suppression of protozoa were compared to quantify effects of protozoa.In all systems examined for this dissertation, predation decreased the amount of biomass, resulting in decreased biofilm thickness and subsequent decreases in system performance. The effects of predation in heterotrophic and nitrifying MABRs were severe due to the increased biofilm sloughing caused by predation. In biofilm growing in a MABR system, biomass near the membrane surface was the most vulnerable to predation, inducing a void layer at the base of the biofilm. This void layer weakened the mechanical stability of the biofilm and promoted biofilm sloughing. Conversely, a void layer was not seen near the base of phototrophic biofilms grown in the MBPR. This discrepancy can be explained by the fact that phototrophs grow via dark respiration at the base of the biofilms where light sources are limited. Unlike the MABRs, the base of the MBPR was likely to have been anoxic. In the last study, an effective and economical method of protozoan control was evaluated. In this method, a novel membrane-based biofilm reactor was implemented where chemicals (e.g., a protozoan inhibitor) were directly supplied to the base of a biofilm via a combination of advection and diffusion. This reactor reduces the loss of chemical to effluent and eliminates the dilution of chemical that occurs in the bulk liquid delivery methods. The novel reactor successfully suppressed predation, resulting in improved reactor performance.