Mediterranean temporary pools represent unique species-rich habitats with many rare and endangered species. The Roque-Haute Natural Reserve is one of the few sites in France with Isoetes setacea Lam., a very rare Mediterranean quillwort, considered as a keystone species determining a priority habitat for the European Union. Land uses changes have favoured the invasion of the pools by several shrub and tree species (e.g., Ulmus minor, Fraxinus angustifolia subsp. oxycarpa). Clearing shrubs in an experimental area of one pool resulted in the increase of I. setacea as compared to control, combining a higher cover in previously occupied quadrats and more quadrats occupied. Litter accumulation had a negative effect on the population of Isoetes but this effect was detectable only in the cleared area. Light attenuation was shown experimentally to be detrimental to the vegetative and regenerative production of I. setacea. Clearing of the shrubs and removal of the litter led to an increase in the I. setacea populations and therefore appears to be an effective technique for restoring these plant communities invaded by shrubs. Long-term shrub control should be ensured by reintroducing sheep grazing in order to enhance the sustainable conservation of this oligotrophic habitat.