Isoëtes malinverniana Ces. et De Not. is a narrow endemic quillwort occurring within channels used for rice fields water supply, in the lowland area of North Italy. The range of I. malinverniana is highly fragmented and in the last 10 years the whole population decreased by more than 80%. This strong decline is assumed to be mainly related to the intensification of agricultural practices, which led to decreasing water quality, alteration of flow regimes and mechanized management. In order to highlight which of these factors may affect population performance and fate (persistence vs. extinction) of the species, plant cover, density and leaf length were measured, and a range of water and sediment parameters were analyzed at the plot scale, within the extant populations and in eight historical sites where I. malinvarniana recently disappeared.At least 4 out of 11 populations, characterized by cover values never exceeding 15% and density hardly approaching 20 plants m −2 , revealed scarce chance for survival, under current conditions. On the basis of discriminant analysis, nutrient enrichment did not result the main predictor of Isoëtes decline, as generally noticed for isoetids, since higher water nitrates, P, K and organic C content in the sediments were found in the sites where I. malinverniana showed the highest performance compared to sites of less viable populations. On the other hand, the high water depth, the strong increase of water flow during the rice growing season and the intensive mechanized management of channels, e.g. cutting of aquatic vegetation and dredging using excavators, were among the most important parameters explaining the disappearance of the species.Our findings may have useful implications for the conservation or restoration of I. malinverniana and other rare aquatic species occurring in running waters of lowland agricultural areas. Hydrological alterations and mechanized maintenance of channels should be restricted where the species still occurs, to improve population performance and seedling survival.