Migratory storks could be vectors of transmission of bacteria of public health concern mediated by the colonization, persistence and excretion of such bacteria. This study aims to determine genera/species diversity, prevalence, and co-colonization indices of bacteria obtained from tracheal (T) and nasal (N) samples from storks in relation to exposure to point sources through foraging. One-hundred and thirty-six samples from 87 nestlings of colonies of parent white storks with different foraging habits (natural habitat and landfills) were obtained (84 T-samples and 52 N-samples) and processed. Morphologically distinct colonies (up to 12/sample) were randomly selected and identified by MALDI-TOF-MS. About 87.2% of the total 806 isolates recovered were identified: 398 from T-samples (56.6%) and 305 from N-samples (43.4%). Among identified isolates, 17 genera and 46 species of Gram-positive and Gram-negative bacteria were detected,Staphylococcus(58.0%) andEnterococcus(20.5%) being the most prevalent genera.S. sciuriwas the most prevalent species from T (36.7%) and N (34.4%) cavities of total isolates, followed byE. faecalis(11.1% each from T and N), andS. aureus[T (6.5%), N (13.4%)].Of N-samples,E. faeciumwas significantly associated with nestlings of parent storks foraging in landfills (p= 0.018).S. sciuri(p= 0.0034) andM. caseolyticus(p= 0.032) from T-samples were significantly higher among nestlings of parent storks foraging in natural habitats. More than 80% of bacterial species in the T and N cavities showed 1–10% co-colonization indices with one another, but few had ≥ 40% indices.S. sciuriandE. faecaliswere the most frequent species identified in the stork nestlings. Moreover, they were highly colonized by other diverse and potentially pathogenic bacteria. Thus, storks could be sentinels of point sources and vehicles of bacterial transmission across the “One Health” ecosystems.Supplementary InformationThe online version contains supplementary material available at 10.1007/s10393-023-01626-x.