A relict population of Isoëtes echinospora Durieu survived a thirty-year period of severe acidification and high concentrations of phytotoxic aluminium (Al) in Plešné Lake (Bohemian Forest, Czech Republic). The population consisted of only adult plants. Sporeling survival and age structure were examined during the population recovery in 2004–2008. Laboratory experiments were conducted to assess the effect of various pH values (4–8) and Al concentrations (0–1000 µg·l–1) on sporeling development. The responses of the sporelings to the experimental treatments were evaluated and compared with those observed in the lake. The experiments showed that an Al concentration higher than 300 µg·l–1, and high acidity (pH 4), inhibit sporeling growth, in particular resulted in a pronounced reduction in absorptive organs (macrogametophyte rhizoids, roots and root hairs). With increasing concentrations of Al and at pH 4, the ratio of the below-ground to above-ground sporeling biomass decreased to less than 1. The responses of the lake sporelings, rooting in the upper sediment layer, were similar to those exposed to 100–300 µg·l–1 of Al in the laboratory, and reflected the Al toxicity of the lake water. The quillworts at Plešné Lake survived because adult plants can tolerate these adverse conditions and are very long-lived. The population recovered when the pH of the water increased to over 5 and the Al concentration decreased to below 300 µg·l–1.