Integration of meroplankton abundance and hydrographic data was employed to relate the Polygordius exolarvae spatial dynamics with different salinity gradients in order to define the factors that regulate the abundance and spatial distribution along the large estuarine system from southern Chile. The present study aims: i) record the abundance and spatial distribution of Polygordius neustonic exolarvae along of the estuaries with different gradients of salinity located between Guafo Channel, southern Chiloé Island (44º S) to Navarino Island (55º S), Chile; ii) connect this distributional pattern to oceanographic parameters to determine if members of this genus have adapted to euryhaline or stenohaline conditions, and iii) establish a comparison between the abundance of Polygordius and others meroplanktonic taxa collected during CIMAR Cruises 16, 18 and 20 Fjords. Neustonic samples were collected during three oceanographic cruises along southern Chilean fjord/channel systems (~ 1,700 km) with different freshwater supply regimes (CIMAR 16: October/November, 2010, 52º to 55º S; CIMAR 18: June/July, 2012, 44º to 47º S; CIMAR 20: October, 2014, 47º to 50º S), providing evidence to relate the influence of surface salinity on the Polygordius exolarvae spatial distribution of abundance. Polygordius exolarvae (average length=2.9 ± 0.8 mm), the most abundant meroplanktonic taxa within the neustonic community (54.04% of total abundance; 66,228 individuals; NTotal=26 stations), was represented at 81% of stations sampled in CIMAR 16 (mean salinity=30.7 psu), showing higher abundance (1,518 ind. x 5 min of horizontal drag) than for other polychaete larvae (10 types) and other meroneustonic taxa; 60% of the abundance of exolarvae during CIMAR 16 was collected around Dawson Island, Magellan Strait. In CIMAR 18 cruise (mean salinity=24.28 psu), abundance of exolarvae was low (3 ind. x 5 min of horizontal drag) and were collected only at 5 stations along the Moraleda Channel (NTotal=31 stations); no exolarvae were collected during CIMAR 20 (Ntotal=39 stations) (mean salinity= 23.26 psu). Polygordius exolarvae have narrow haline/thermal requirements during their pelagic life, where sills and island mass effect could produce a restricted and aggregated spatial distribution in some areas of the study zone.