The common carp (Cyprinus carpio) is a non-native fish species in many parts of the world which has negative impacts on freshwater environments including plant loss, re-suspended sediment, and altered nutrient flux. Eradication of common carp can be extremely difficult and conventional management efforts have focused on control or containment, achieved with barriers that decrease or eliminate access to specific habitats. Here, we examined biological traits of common carp that can be exploited with barriers to control populations and minimize ecological impacts; however, an important consideration during barrier design and implementation are impacts on non-target, native species (i.e., selective fragmentation). Phenology, such as differences in reproductive timing, could be used to operate barriers to minimize impacts on some native species. Sensory ability could also be exploited in cases where common carp is more sensitive to electrical, acoustic, visual and/or chemical stimuli. Differences in morphology of common carp compared to native species could contribute to barrier design (e.g., 5.0 cm spacing in vertical bars screens), whereby larger common carp are excluded but many native species can pass. Behaviour, such as common carp jumping, can also be exploited to separate carp from native species with modified barriers. We explore cases of each trait being used through diverse case studies: phenology (Sea Lamprey Control Program); sensory capability (carbon-dioxide deterrents); morphology (vertical bar screens); and behaviour (the Williams’ cage). The approach taken here with common carp can be applied to other aquatic non-native species to assess the potential for barriers to reduce associated negative impacts on native fish species with selective fragmentation.