Background: Biofilms in chronic rhinosinusitis (CRS) patients are associated with recalcitrant disease patterns. Citric acid/zwitterionic surfactant (CAZS) has been shown to have significant efficacy at in vitro biofilm eradication. Unique hydrodebrider systems have been shown to have effective antibiofilm efficacy. The aim of this study was to evaluate the efficacy of the CAZS/hydrodebrider treatment on Staphylococcus aureus biofilms in the sheep model of CRS. Methods: Forty-two sheep frontal sinuses were inoculated with S. aureus, followed by 7 days of biofilm growth. Sinuses were randomized to one of nine treatment groups: control, hydrodebrider with saline or CAZS (killed on day 0 or day 7 posttreatment), CAZS, or saline flush (killed on day 0 or day 7 posttreatment). Confocal scanning laser microscopy (CSLM) was used to confirm extent of biofilm reduction. Samples of each sinus were taken, assessing cilia morphology using electron microscopy. Results: A mean of 37.22 ± 9.65% of control (no treatment) CSLM images taken showed biofilms. Both CAZS flush and CAZS/hydrodebrider treatments showed initial improvements in biofilms but biofilm regrowth followed treatment, 14.74 ± 9.58% to 18.91 ± 12.14% and 15.60 ± 13.92% to 24.70 ± 3.66%, respectively (p > 0.05). Saline/hydrodebrider treatments showed a nonsignificant improvement in biofilm treatment, which was maintained, 18.34 ± 11.85% to 12.04 ± 10.28% (p > 0.05). Cilial morphology grade was significantly worse in the CAZS treatment groups (p > 0.05). Conclusion: CAZS solution (with and without a hydrodebrider system) can significantly adversely affect cilia morphology. The hydrodebrider system, when combined with saline, may be a useful treatment adjunct for mucosal biofilms.