Potamogeton rutilus Wolfg. is a rare threatened macrophyte which, within the British Isles, is confined to oligo-mesotrophic Scottish lochs. The species has been lost from some of its former recorded sites, thought due to eutrophication and other environmental habitat changes. The plants limited distribution may be partly related to its lack of seed production that may limit long distance bird seed dispersal. P. rutilus appears to be reliant on clonal growth for reproduction, so may have a reduced genetic diversity that can reduce fecundity. To assist the development of strategies for the future conservation of P. rutilus, a series of investigations was carried out to reveal the autecological factors that influence the plant’s distribution and survival. In summing up the main findings of the investigation, it was found that Scottish and Finnish P. rutilus have different trophic plant community types, with Scottish P. rutilus inhabiting less nutrient rich oligo-mesotrophic lochs than the more nutrient rich, eutrophic, Finnish P. rutilus habitats. Salinity may have caused P. rutilus to be lost from some of its former machair lochs. P. rutilus abundance and macrophyte diversity significantly declined with reduced light availability in lochs. The growth experiments revealed that P. rutilus turion size is a good measure of plant fitness and fecundity and eutrophic phosphate conditions, under a half-light regime, produced optimum P. rutilus turion growth. The genetic investigations suggest there is limited gene flow between P. rutilus populations and this could be due to the lack of seed production for inter-population seed dispersal. However, P. rutilus does not totally rely on clonal growth for reproduction, as genetic evidence suggested there was some degree of sexual reproduction in some populations.