In fjord systems, freshwater inputs occur by ice melting and river discharge, affecting seawater salinity along fjord and adjacent waters, and potentially the ecology of early life stages of marine fish occurring in the area. During austral spring 2008, a bio-oceanographic cruise was carried out in southern Chile between 47°00′ and 50°09′S, an area influenced by Baker River discharge and ice melting of Northern and Southern Ice Fields, the largest glaciers from Patagonia. Surface salinity and temperature ranged from 1.22 to 32.80, and from 8.11 to 10.68°C, respectively. Larval lightfish Maurolicus parvipinnis (Sternoptychidae) and Falkland sprat Sprattus fuegensis (Clupeidae) were the dominant species, with abundances of 2.2-39.9 larvae 10 m −2 and 3.4-77.1 larvae 10 m −2 , respectively. Postflexion stages of both species were collected mainly in surface density fronts. Otolith-based growth analyses estimated linear growth rates of 0.136 mm day −1 for M. parvipinnis of 4.1-15.1 mm, and 0.448 mm day −1 for S. fuegensis of 5.4-20.5 mm. Recent Otolith Growth Index (ROGI), based on the residual analysis of the relationship between increment width of outermost five microincrements and otolith radius, indicates that larval M. parvipinnis collected in low salinity waters showed a reduction of its recent growth rate compared those collected in saltier waters. Also, ROGI was positively correlated with salinity of the water column for larval M. parvipinnis. Gut content analysis showed that large larvae collected near sources of freshwater had lower number of prey in its guts and preyed on different items than fish larvae collected in saltier waters. Therefore, freshwater inputs from rivers and glaciers from Patagonia affected horizontal distribution, recent growth and feeding of larval fish in fjords and channels of southern Chile.