Cod and sprat are the dominant fish species in the Baltic pelagic ecosystem, both of great economic importance and ecologically strongly interlinked. Management of both species is challenged by highly variable recruitment success. Recent studies have identified predation and hydrographic conditions during the egg phase to be of critical importance. Two years of extensive field investigations in the Bornholm Basin, central Baltic Sea, were undertaken. In 2002, a typical stagnation situation characterized by low salinity and poor oxygen conditions was investigated, and in early 2003, a major inflow of North Sea water completely changed the hydrographic conditions by increasing salinity and oxygen content, thereby altering ecological conditions. The goal was to quantify egg mortality caused by predation and hydrography, and to compare these estimates with independent estimates based on cohort analysis. Results indicated high intra-annual variability in egg mortality. Cod and sprat egg mortality responded differently to the major Baltic inflow: mortality related to hydrographic conditions increased for sprat and decreased for cod. On the other hand, predation mortality during peak spawning decreased for sprat and increased for cod.