We report on the emergence of the epibiotic barnacle Xenobalanus globicipitis in Guiana dolphins (Sotalia guianensis) from Sepetiba Bay, Rio de Janeiro, Brazil, in September 2018, six months after a lethal morbillivirus epidemic. Small boat surveys were conducted at the entrance and in the interior of the bay from January 2018 to February 2021. Dolphins were photo-identified and classified according to overall spatial use of the Bay. We examined the potential influence of the period and habitat on the prevalence of X. globicipitis. The overall prevalence of the barnacle was 38.7% in 214 dolphins. X. globicipitis was not observed in 99 individually identified dolphins from January to August 2018 (first period) but was seen on 83 of the 194 (42.8%) dolphins photographed from September 2018 to February 2021 (second period). Moreover, in 22 individuals repeatedly photographed during both periods, prevalence was 0% and 91% during the first and second period, respectively. Prevalence was the highest in the dolphins using the entrance of the Bay (55.0%, N = 140), intermediate in animals using equally both the entrance and interior area (42.9%, N = 47), and the lowest (6.4%, N = 7) in those using the interior area only. The calves of five females infested with X. globicipitis were free of barnacles. Based on repeated photographs of barnacles at different growth stage on six dolphins, the periods between first and last sight with the epibiont were (in increasing order) 29, 32, 40, 51, 68 and 78 days. A conservative estimation from the initial settlement to sexual maturity was around 40–45 days. Three individuals of X. globicipitis collected on a stranded dolphin measured 65 mm, 61 mm and 35 mm, the largest recorded size to date. The two large individuals had incubated embryos while the smaller one presented developing gonads. Poor health and an impaired immune response in the dolphins that had survived the morbillivirus epidemic may have favored the introduction of the barnacle, but biotic and abiotic factors could also had played an important role. This paper documents the colonization of an estuarine area by X. globicipitis following ecological changes.