1. Managing populations of predators and their prey to achieve conservation or resource management goals is usually technically challenging and frequently socially controversial. This is true even in the simplest ecosystems but can be made much worse when predator–prey relationships are influenced by complex interactions, such as biological invasions, population trends or animal movements. 2. Lough Neagh in Northern Ireland is a European stronghold for pollan Coregonus autumnalis, a coregonine fish and for river lamprey Lampetra fluviatilis, which feeds parasitically as an adult. Both species are of high conservation importance. Lampreys are known to consume pollan but detailed knowledge of their interactions is scant. While pollan is well known to be a landlocked species in Ireland, the life cycle of normally anadromous river lamprey in Lough Neagh has been unclear. The Lough is also a highly perturbed ecosystem, supporting several invasive, non-native fish species that have the potential to influence lamprey–pollan interactions. 3. We applied stable isotope techniques to resolve both the movement patterns of lamprey and trophic interactions in this complex community. Recognizing that stable isotope studies are often hampered by high-levels of variability and uncertainty in the systems of interest, we employed novel Bayesian mixing models, which incorporate variability and uncertainty. 4. Stable isotope analyses identified trout Salmo trutta and non-native bream Abramis brama as the main items in lamprey diet. Pollan only represented a major food source for lamprey between May and July. 5. Stable isotope ratios of carbon in tissues from 71 adult lamprey showed no evidence of marine carbon sources, strongly suggesting that Lough Neagh is host to a highly unusual, nonanadromous freshwater population. This finding marks out the Lough’s lamprey population as of particular scientific interest and enhances the conservation significance of this feature of the Lough. 6. Synthesis and applications. Our Bayesian isotopic mixing models illustrate an unusual pattern of animal movement, enhancing conservation interest in an already threatened population. We have also revealed a complex relationship between lamprey and their food species that is suggestive of hyperpredation, whereby non-native species may sustain high lamprey populations that may in turn be detrimental to native pollan. Long-term conservation of lamprey and pollan in this system is likely to require management intervention, but in light of this exceptional complexity, no simple management options are currently supported. Conservation plans will require better characterization of population-level interactions and simulation modelling of interventions. More generally, our study demonstrates the importance of considering a full range of possible trophic interactions, particularly in complex ecosystems, and highlights Bayesian isotopic mixing models as powerful tools in resolving trophic relationships.