The horizontal distribution of the most abundant species (four in winter, five in spring) showed decreasing abundances in the north–south direction in winter and spring. Peak abundances occurred in the northern microbasins (Reloncavxed; Fjord, Reloncavxed; and Ancud gulfs), where the water column stability, phytoplankton and zooplankton abundance were higher, compared with the southern microbasins (Corcovado Gulf, Boca del Guafo). During the spring higher jellyfish abundance season, the vertical distribution of the dominant species (except M. atlantica) showed peak values at mid-depth (30–50 m) and in the deepest sampled layer (50–200 m). This vertical distribution pattern reduced seaward transport in the shallowest layer through estuarine circulation and also limited mortality by predation in the more illuminated shallow layers. Thus, jellyfish were able to remain in the interior waters during the season of maximum biological production.