The distributions of micronekton layers in the Balearic Sea (western Mediterranean) were investigated by acoustic methods. Two multidisciplinary surveys were carried out in late autumn 2009 and summer 2010, recording acoustic, biological and hydrographic data. We described the acoustic layers and migratory behavior, sampled species and water masses processes. Acoustic modeling of gas-bearing organisms was employed to explain differences between acoustic estimates and sampled abundances. The influence of environmental variables on the vertical distribution and migration pattern of these organisms was analyzed. The thermocline depth was related to the preferred depth for migrating myctophids, while non-migrant species dwell in the oxygen minimum zone of the water column both in late autumn and summer periods.