Functioning of hearing organs and ENT microflora composition were investigated in 10 healthy male subjects (25–36 y.o.) who volunteered for a 7-day dry immersion as a model of the physiological effects of microgravity. The functional state of the hearing organs was assessed with the registration of distortion product oto-acoustic emission (DPOAE), and tympanometry. Specifically, assessed were the signal-to-noise ratio (SNR) of the oto-acoustic response (dB), middle ear pressure (daPa) and tympanogram maximal compliance (ml). To identify and count ENT microbial cultures, samples were gathered from the nasal and pharyngeal membranes and external skin of the auditory meatus. The eubiotic index was used to detect changes in the microflora composition. Changes in the hearing organ functioning included a SNR decrease in DPOAE of the low-frequency band (p ≤ 0.05), increase of the middle ear pressure (p ≤ 0.05) and an obvious downward trend of the maximal compliance. Dynamic microbiocenosis assessment discovered several negative changes such as a reduction in the number of protective microorganisms and growth of the number of opportunistic groups. The eubiotic index value was below one. These changes demonstrate a potential negative effect of modeled microgravity on the ENT microflora functioning and composition. Methods of dynamic assessment and control of the hearing organ and ENT microbiocenosis would be appropriate for use in monitoring of cosmonauts' health.