Microparasites and epibionts have important implications for the ecology and evolution of their zooplankton host populations. Many parasites and epibionts produce resistant spores that infect new hosts upon intake. We explored the hypothesis that these spores build up dormant stage banks that remain infective for several years (decades). In laboratory experiments, we exposed Daphnia magna to sediments taken from different depths in sediment cores from four different shallow water bodies. All samples analyzed contained infective stages of epibionts, suggesting that dormant stage banks remain infective for decades. Microparasite infections from old sediments were only obtained in one of the four ponds studied. We found mainly the bacterium Pasteuria ramosa but also a yet undescribed microsporidium. We discuss the implications of long-lasting spore banks for the disease dynamics and coevolution in the Daphnia-microparasite system.