The critical information for conserving endangered species is to identify how different niche dimensions affect the bottlenecks in the life history stages of populations. However, it is often difficult to quantify how each niche dimension affects different life history stages because environmental factors may affect each fitness component of organisms to various degrees. Here, we applied the recently developed hypervolume method that follows the idea of Hutchinson’s n-dimensional hypervolume. We analyzed the niche space of different life history stages of the endangered landlocked salmon Oncorhynchus masou formosanus, the most southerly distributed of all salmonoids. We found no direct effect of water pollution on adult population density but a significant negative effect on their embryo hatching rate. Surprisingly, the niche hypervolume analysis showed that the size of embryo niche hypervolume was only 42% and 45.3% of the natural redd density or adult population density, respectively. This result suggests that water quality requirements during the embryonic stage are a key bottleneck in the life history stages of O. m. formosanus. Our results suggest that understanding the behavioral and physiological mechanisms that influence crucial life history stages in the wild is critical to developing effective conservation programs, and the niche hypervolume is a valuable method to achieve this.