Investigations of predator–prey dynamics have largely focused on quantifying predation rates, yet achieving an appropriate sample to quantify predation is difficult when prey populations are small and individuals are rare. Moreover, quantifying rates of predation does not necessarily provide solutions for protecting threatened populations from predation. We used predator abundance and fine-scale predator–prey spatial overlap to identify trends in predation risk from cormorants, Phalacrocorax, to adults of the endangered Macquarie Perch, Macquaria australasica, in Cotter Reservoir, Australia. We made observations of cormorants at Cotter Reservoir between February 2008 and July 2009 to estimate abundance and spatial distribution. We used radiotelemetry to locate adult Macquarie Perch. Cormorant abundance was highest in spring and summer. Increased cormorant abundance corresponded with an increase in the fine-scale overlap of the distributions of Macquarie Perch and cormorant within the reservoir. Overlap was highest in the upstream section of the reservoir, which is characterized by shallow water (<5 m depth). Increased overlap corresponded with congregation of Macquarie Perch in the upper reservoir and movement toward the source river for spawning. Our results provide valuable insight into when and where predation is most likely to occur, thereby allowing conservation efforts to be tailored to protect this threatened fish population effectively.