Quillworts (Isoëtes) represent highly specialised flora of softwater lakes, i.e., freshwater ecosystems potentially sensitive to acidification. In this paper, we combine a review of previous studies and our new results to address unrecognised reproduction strategies of quillworts to overcome long-term environmental stresses. These strategies play an important role in the plant’s ability to overcome atmospheric acidification of freshwaters, protecting the plants until their environment can recover. Environmental drivers of recovery of Isoëtes echinospora and I. lacustris were studied in two acidified lakes in the Bohemian Forest (Central Europe). Both populations survived more than 50 years of severe acidification although they failed to recruit new sporelings. Their survival depended entirely on the resistance of long-living adult plants because the quillworts do not grow clonally. During the past two decades, a renewal of the I. echinospora population inhabiting Plešné Lake has been observed, while no such renewal of I. lacustris, dwelling in Černé Lake, was evident, despite similar changes in water composition occurring in both lakes undergoing advanced recovery from acidification. Our in vitro experiments revealed that the threshold acidity and toxic aluminium concentrations for sporeling survival and recruitment success differed between I. echinospora (pH ≤4.0 and ≥300 μg L^-1 Al at pH 5) and I. lacustris (pH ≤5.0 and ≥100 μg L-1 Al at pH 5). The higher sensitivity of I. lacustris to both stressors likely stems from its year-long germination period and underlines the risk of exposure to chronic or episodic acidification in recovering lakes. In contrast, the shorter germination period of I. echinospora (2–3 months) enables its faster and deeper rooting, protecting this quillwort from periodic acidification during the next snowmelt. Our study brings novel insights into widely discussed environmental issues related to the long-term degradation of softwater lakes, which represent important hotspots of pan-European biodiversity and conservation efforts.