Isoëtes echinospora, a submerged aquatic quillwort, is native in northern latitudes and a rare glacial relict in mountain lakes in temperate Central Europe. A relic population of this quillwort in the Plešné jezero lake has recovered recently from a 30-year period of failure to reproduce caused by acidification. Early ontogenetic stages of the quillwort are considered to be the most vulnerable to environmental changes. Therefore, the objective of this study was to investigate the phenology of germination of I. echinospora. In a two-year experiment, we examined the time course of germination of micro- and macrospores and establishment of sporelings under (i) natural in situ conditions in the Plešné jezero lake and (ii) at various temperatures (6–17 °C) in the laboratory. We developed a mathematical model that describes the temperature-specific temporal changes in the early ontogeny of I. echinospora. Our experiments clearly show that spores do not germinate at once but gradually over time if exposed to favourable temperatures. Generally, percentage germination tended to increase during the course of a season under most temperature regimes but was inhibited at the lowest temperature. With increasing temperature, microspores germinated earlier and more successfully than macrospores, as described by the model. Sporelings also developed faster at the higher temperature. However, the highest temperature used in the experiments (17 °C) desynchronized the phenology of germination in I. echinospora as it resulted in the two types of spore not being available for fertilization at the same time. Thus, climate change might affect interactions between temperature and the phenology of quillwort reproduction and threaten the survival of this species in Central Europe.