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The brackish water Baltic Sea is strongly influenced by irregular saline water inflows. Fewer inflow events since the 1980s have resulted in a decrease in salinity, and will according to predicted climate change continue to decrease. The newly described Baltic flounder Platichthys solemdali has adapted to reproduction at low salinity conditions since it colonized the Baltic Sea 7000 years BP; in the area studied (ICES SD 3d 28.2) spawning occurs at 3–20 m depth at ca 7 psu. Here we monitored variability in year-class strength as newly settled 0-gr fish in three coastal nursery areas, and compared obtained recruitment indices with prevailing temperature and salinity conditions. 0-gr abundance indices varied considerably between years, from 1 to 90, 10–296 and 17–86 at the respective sampling site, and showed strong accordance with the age structure of the adult stock. Variability in temperature showed no effect, but stronger and weaker year-classes respectively were related to variability in salinity in the range 6.6–7.1 psu with stronger year-classes at >6.8 psu. This coincides with variability in spermatozoa motility, fertilization rates and early egg development at different salinities and suggests that the year-class strength may be set already at the egg stage. Thus, only small changes in salinity at spawning may affect reproductive success and ultimately stock development. The potential effects on stock abundance and distribution facing climate change call for changes in future fishing patterns as well as adaptations in management to prevent stock collapse.