Reducing water salinity towards iso-osmotic conditions is a common practice applied in euryhaline fish farming to limit osmoregulation costs and enhance growth. In this respect, the present study investigated the timing of salinity reduction in an abrupt manner during European eel (Anguilla anguilla) larval culture by examining associated impacts on morphological and molecular levels. Larvae from 3 different parental combinations (families) were reared at constant 36 psu for 6 days (control) or subjected to a direct reduction to 18 psu on 1, 2, or 3 days post-hatch. Overall, salinity reduction enhanced growth and survival, resulting from more efficient energy resource utilization. In the control group, expression of growth-related igf2 remained constant, demonstrating a steady growth progression, while igf1 expression increased over time only for the salinity reduced treatments, potentially qualifying as a useful biomarker for growth performance. Even though each parental combination seems to have a different capacity to cope with salinity alterations, as observed by family-driven water-transport-related aquaporin (aqp1, aqp3) gene expression, it could be inferred that the abrupt salinity change is generally not stressful, based on non-upregulated heat shock proteins (hsp70, hsp90). However, the applied salinity reduction (irrespective of timing) induced the development of pericardial edema. As such, we conclude that despite the positive effect of salinity reduction on early growth and survival, the long-term benefit for eel larval culture lies in establishing a protocol for salinity reduction, at a precise developmental time point, without causing pericardial malformations.