We investigated the environmental drivers of larval abundance of anchovy Engraulis encrasicolus and sardine Sardinops sagax in Algoa Bay, Eastern Cape (South Africa). This study comprised a pre-drought post-drought time period, comparing the responses of the fish larvae to different factors before and after the drought. The current study presents, for the first time, which environmental variables are affecting the anchovy and sardine larvae populations in the region. Easterly wind speed and zooplankton density were the only environmental variables that presented a significant change between the pre- and post-drought periods, increasing after the drought. Generalized additive models (GAMs) were used in order to explore the effects that environmental factors might have in the abundance of anchovy and sardine larvae in Algoa Bay. Specifically, the GAM that best explained the deviance of the anchovy larvae dynamics included the covariates rainfall, easterly wind speed, Chl a concentration, sardine larvae abundance and the interactions SST*Chla and sard*SST. The GAM best explaining sardine larvae abundance included only the easterly wind speed as a covariate. This model showed that there was a positive relationship between the higher values of wind speed and sardine larvae abundance.