Chronic, severe otitis media was diagnosed in four Atlantic harbor seals (Phoca vitulina concolor), three of which were stranded animals undergoing rehabilitation. All seals presented with unilateral purulent aural discharge that would intermittently recur despite prolonged topical and systemic antimicrobial therapy. Aerobic culture from aural discharge isolated multidrug-resistant organisms in all seals, including Pseudomonas aeruginosa, Staphylococcus pseudintermedius, Klebsiella pneumoniae, and/or Enterococcus faecalis. Computed tomography was used in three cases to confirm otitis media and positive contrast ear canalography was used in one case to confirm tympanic membrane rupture. Given the persistent nature of otitis, surgical intervention in the form of a total ear canal ablation and lateral bulla osteotomy (TECA-LBO) was indicated. Surgery was successful in achieving complete clinical resolution of otitis in all seals. Postoperative complications included temporary unilateral paralysis of the left nare (2/4) and a transient left ptosis (1/4). Partial to complete surgical site dehiscence occurred in all cases; however, complete healing was achieved by second intention in 60 d or less. One rehabilitated seal was fitted with a satellite tag that confirmed normal swimming and diving patterns post release. In harbor seals, TECA-LBO can be performed safely to treat persistent cases of otitis media and should be considered in cases of chronic otitis that are not responsive to medical management.