Sixteen sites in China where Ceratopteris pteridoides occurs based on historical records and/or from observations were surveyed during preliminary field surveys. Eight previously recorded populations were found to have been extirpated. Decline in natural populations of C. pteridoides has resulted from the destruction or complete loss of its primary habitat. Analysis of 17 parameters of water quality indicated that differences in pH and dissolved oxygen might be principal factors determining the distribution and occurrence of C. pteridoides. The sites of the extirpated populations had higher water pH values than those of the sites of the extant populations (p < 0.05). The value of dissolved oxygen concentration at the sites of the extirpated populations was lower than at the sites of the extant populations (p < 0.05). The degeneration of primary habitats, a decline in the area of wetland coverage and deterioration of water quality caused by human activities are identified as the likely key factors responsible for the reduction in C. pteridoides populations. Because the habitat and population characteristics of eleven remaining populations were different, different sites should adopt different conservation methods as appropriate. Some small populations could be conserved by establishing conservation areas; other relatively large populations could be conserved by establishing nature reserves.