Dispersal of bacteria from a biofilm in the middle ear, serving as a bacterial reservoir, could explain the recurrent and chronic nature of chronic suppurative otitis media (CSOM). The objective of this study is to investigate if the same strains of bacteria could be detected in repeated episodes of otorrhea in CSOM. In a prospective case series at a primary healthcare clinic in Nuuk, Greenland, patients with more than 14 days of otorrhea were included consecutively. Samples for culturing and biofilm analysis were taken at enrollment and at any subsequent episode with otorrhea. Participants were treated with daily saline irrigation and Ciprofloxacin eardrops for 7–14 days. Biofilm was identified in otorrhea in 81% (17/21) of participants at enrollment. Multispecies infections dominated with Non-typeable Haemophilus Influenzae (NTHI), Staphyloccocus aureus, and anaerobes being the most frequent pathogens. After the initial treatment, 19 (90%) had dry ears. Median observation period was 140 days (range 14–280) where 13 participants had one or more recurrences. Median time to first recurrence was 60 days (range 14–197). Among the 13 with recurrence, three individuals had the same genotype of bacteria at a subsequent episode. Another two had the same phenotype (NTHI). The remaining eight had new multispecies infections. We confirmed a high rate of biofilm in CSOM. However, the clinical implication might be of minor importance when treating with irrigation and antibiotic eardrops, as recurrent episodes of otorrhea were dominated by new pathogens in each episode.