Many organisms that live in inland standing waters produce dormant life stages that can accumulate in propagule banks to survive temporarily unfavourable periods. These egg banks have important effects on the ecology of populations and communities in terms of phenology, population densities, the probability of extinction, species diversity and habitat connectivity in time and space. They also have important consequences for the evolutionary versatility of populations. Although diapause and dormant egg banks in freshwater zooplankton have been studied for several decades, little is known about the quantitative contribution of egg production and hatching to yearly egg bank budgets and their seasonality in natural ponds and lakes. Here we quantified inter- and intra-annual variation in hatching and dormant egg production in the water flea Daphnia magna in two natural shallow ponds in Flanders (Belgium) using high-intensity sampling and in situ measurements. Hatching started in spring and occurred in several bouts (April–July), accumulating to a yearly average total of 3.5 × 103 hatchlings m−2. Dormant egg production occurred in one-to-three bouts mainly during late spring and summer (May–August), resulting in a total yearly production ranging from 1.2 × 104 up to 17.3 × 104 ephippia m−2. In both years, there was an average surplus of 3.14 × 104 and 15.24 × 104 ephippia produced m−2 for ponds OM2 and OM3, respectively, contributing to the accumulation of the persistent egg bank. We discuss the ecological and evolutionary consequences of both the high number of ephippia that are produced and the high number of hatchlings at the start of each growing season.