Pseudomonas aeruginosa frequently causes chronic lung infection in individuals with muco-obstructive airway diseases (MADs). Chronic P. aeruginosa infections are difficult to treat, primarily owing to antibiotic treatment failure, which is often observed in the absence of antimicrobial resistance. In MADs, P. aeruginosa forms biofilm-like aggregates within the luminal mucus. While the contribution of mucin hyperconcentration towards antibiotic tolerance has been described, the mechanism for mucin driven antibiotic tolerance and the influence of aggregates have not been fully elucidated. In this study, we investigated the contribution of flagellar motility towards aggregate formation as it relates to the diseased mucus environment. We found that loss of flagellar motility resulted in increased P. aeruginosa aggregation and tolerance to multiple classes of antibiotics. Further, we observed differential roles in antimicrobial tolerance of the motAB and motCD stators, which power the flagellum. Additionally, we found that control of fliC expression was important for aggregate formation and antibiotic tolerance as a strain constitutively expressing fliC was unable to form aggregates and was highly susceptible to treatment. Lastly, we demonstrate that neutrophil elastase, an abundant immune mediator and biomarker of chronic lung infection, promotes aggregation and antibiotic tolerance by impairing flagellar motility. Collectively, these results highlight the key role of flagellar motility in aggregate formation and antibiotic tolerance and deepens our understanding of how the MADs lung environment promotes antibiotic tolerance of P. aeruginosa.