Summary Small rosette plants in oligotrophic, softwater lakes, such as Lobelia dortmanna and Littorella uniflora, have highly permeable root surfaces that allow acquisition of CO2 from the sediment for photosynthesis. In the absence of an oxygen supply from photosynthesis, these permeable roots increase the risk that the plants are deprived of oxygen when sediments turn anoxic at night, or more permanently if there is organic enrichment. We hypothesised that isoetids, despite their preference for pristine, well‐oxygenated habitats, should be relatively tolerant to tissue anoxia and that L. dortmanna should be more tolerant than L. uniflora because the impermeable leaf surfaces of L. dortmanna prevent the entry of oxygen from aerated lake waters and generate higher risks of anoxia in plant tissues at night. Metabolism, survival and subsequent growth of both species were unaffected by darkness under oxic conditions for 8 days at 20 °C. All L. dortmanna individuals and 60% of L. uniflora individuals survived exposure to anoxic water in the dark for 5 days. Anoxia reduced respiration during exposure, depressed the quantum efficiency of Photosystem (PS) II immediately after anoxic exposure and reduced growth during a 24‐day recovery phase. Plant growth under recovery declined with increasing length of anoxia from 2 to 8 days, and L. uniflora was more affected than L. dortmanna. Overall, the two species were very tolerant to oxic, dark exposure and also survived prolonged anoxia, probably because of inherently low respiratory maintenance costs. Lower metabolism of L. dortmanna than L. uniflora probably contributes to its higher tolerance to tissue anoxia, while higher leaf permeability to oxygen uptake from the water may help L. uniflora to survive recurrent sediment anoxia at night during summer.