Brasenia schreberi J. F. Gmel. (Cabombaceae), a perennial freshwater macrophyte characterized by a thick mucilage on all underwater organs and especially young buds, has been widely cultivated as an aquatic vegetable in China for many years but is now listed as an endangered species due to anthropogenic impacts and habitat loss. Recent studies have demonstrated that different B. schreberi populations in China have low levels of genetic diversity but significantly different mucilage contents (MucC). Considering the importance of mucilage on both economic and ecological aspects, we examined mucilage-environment relationships in three B. schreberi cultivation sites. The results indicated that water permanganate index (CODMn), total N (TNw), electrical conductivity (ECw), dissolved oxygen (DOw), sediment organic carbon (SOC) and total N (TNs) were significant factors, which explained 82.2% of the variation in mucilage accumulation. The MucC and mucilage thickness (MucT) as well as single bud weight (SBW) of B. schreberi showed negative relationships with CODMn, TNw and ECw but positive relationships with SOC and TNs. Besides, high temperature may have a negative impact on mucilage accumulation of the species. Our study demonstrated that the mucilage accumulation of B. schreberi required good water quality and nutrient-enriched sediments, suggesting that habitat conservation, especially the quality of water, is important for maintaining B. schreberi populations.