The recently launched Daily Egg Production Method (DEPM) surveys to estimate the spawning stock biomass (SSB) of the northern Aegean Sea anchovy stock are presented and variability in plankton and adult parameters is analyzed for the yearly applications of 2003, 2004, 2005, 2006 and 2008. Anchovy spawned mainly over the continental shelf of the Thracian Sea in the east (directly affected by Black Sea waters), and the semi-enclosed Thermaikos Gulf and Evoikos Gulf in the west. The surveyed area was therefore post-stratified into an eastern and western region and DEPM parameters, which, in certain years, differed markedly between the two areas, were estimated separately for the two strata. To increase precision of the daily egg production estimates, both eggs and yolk sac larvae were used assuming that the mortality rate does not change between the egg and yolk sac larval stage. Embryonic mortality increased as a power function of temperature. The estimation of spawning fraction was based on the postovulatory follicles (POFs) method and was particularly complicated due to the presence of strong thermoclines and diel vertical migration of the fish: POF absorption was very fast during the night, when fish were located above the thermocline (>20°C), but relatively slow during the day, when fish were close to the bottom at ∼14–15°C. Mean relative batch fecundity was significantly related to somatic condition (energy reserves) whereas spawning frequency was related to liver condition (presumably, direct food intake). In comparing daily specific fecundities (DSFs) with concurrent estimates of mesozooplankton biomass and total anchovy biomass (independently derived from acoustic sampling) evidence for strong density-dependence in DSF emerged. Density-dependent use (expansion–contraction) of the spawning habitat (SA), indexed by the ratio CV(SA)/CV(SSB), was relatively low but density-dependency of egg production CV(DSF)/CV(SSB) was particularly high in the N. Aegean Sea compared to the more productive Bay of Biscay or upwelling regions.