Factors affecting the decline in Potamogeton dentatus, which is a critically endangered submerged perennial plant, at an irrigation pond in Kitakyushu, the sole natural habitat of the species in Japan, were examined. The water flowing into the pond is very clear, and the physicochemical properties of the water of the pond are suitable for growth of the species, indicating that water quality is not the main factor in the drastic decline of the species at the pond. This special clarity of inflow to the pond may be why it has not been fully drained for several decades. Lack of drainage has made the quantity and quality of the bottom sediment unsuitable for growth of the species. In fact, bottom sediments with fine particles have accumulated and eutrophicated at the pond. Thus, the eutrophicated bottom sediments are likely to be the proximate factor causing the decline of P. dentatus at the pond. More broadly, socioeconomic changes in the 1960s and the special nature of the pond are the ultimate factors causing this decline.