As domestic animals, the trusting nature of koi often puts them at risk of predation from wild or feral animals in their environment. Of the mammalian threats are raccoons, which will enter shallow dished ponds in suburban and even urban areas and catch koi, and feral cats, which will occasionally catch, but often only cause linear lesions on the dorsal area. The best protection against these threats is proper koi pond design, with pond edges dropping off sharply to an 18" (46 cm) depth, eliminating wade-in areas. Existing shallow ponds must be netted at night. The North American river otter (Lontra canadensis) and the mink (Neovison vison) can both be very efficient predators of koi. As their historic ranges have been greatly affected by habitat loss and hunting, encounters are now rare except in rural areas. Control can be difficult, with secure fencing being the most effective. Muskrats (Ondatra zibethicus), although rodents and therefore not strictly predators, have been included because of deaths in koi due to pond drainage. The muskrat will create a burrow alongside the pond and then chew through the liner to create one or more underwater entrances as part of their predator avoidance system. In areas where this rodent is found, ponds should be concrete lined to a depth of 4' (122 cm). As to reptiles and amphibians, turtles can present injuries, primarily to fins, where a characteristic V-shaped notch will be seen. These wounds can be the origin of secondary bacterial infections. Species appearing intermittently into koi ponds are the snapping turtles (Chelydra serpentina, Macrochelys temminckii) and the soft-shelled turtles (Trionychia spp.). Additionally, pond owners will sometimes attempt to integrate common collected and captive bred species, such as the red-eared slider (Trachemys scripta elegans) and the painted turtle (Chrysemys picta) into their ponds. Due to their tendency to nip fins, this should be discouraged. One amphibian, the bullfrog (Rana catesbeiana), in those habitats where it is found, will often migrate to koi ponds during rainy periods. Large specimens can often capture and eat young koi up to about 6" (15 cm) in size. Management of this threat in ponds is difficult: where these pests are found, young koi should be isolated in protected aquasystems until large enough to be placed in the pond.

The largest groups of predators are various species of birds. The most frequently encountered pests are the herons. This group of wading birds includes the green heron (Butorides virescens) and night heron (Nycticorax nycticorax), both of which hunt at dusk or after dark and the great white and great blue herons (Ardea herodias), which are stealth hunters by day. Normally inhabitants of marshes and shallow wetlands, their usual prey are frogs. In early spring, for migratory individuals to northern areas, they will identify koi ponds from the air. In southern locations, they are year round residents. In dished ponds with wade-in areas less than 18" (46 cm) deep, they will enter slowly, then remain motionless with their wings extended and neck flexed. In ponds with minimal shading, koi will soon congregate under this shadow and they can be rapidly speared. Once caught, few koi will escape. Occasionally, when one does, a characteristic lesion of one or two deep focal puncture wounds or a single linear lesion may be seen on the dorsal aspect. Although these lesions can resemble the more frequently seen koi bacterial ulcers, they are always found above the lateral line and ulcers are often seen below. The best protection is again koi pond design featuring sharply dropping pond edges to a depth of 18" (46 cm) to eliminate the wade-in area, as herons do not wade in water deeper than that. Additionally, always provide for 1/3 of the pond surface to be shaded. In existing shallow ponds, automated scares such as photocell-activated water jets provide some protection, but are often evaded. Surface floating devices, like Pond'toons or floating islands, can be used to cut off wade-in areas. The most consistent protection is with monofilament lines as described below. Hawks, such as the red-tailed hawk (Buteo jamaicensis), are normally hunters of squirrels and rabbits. In suburban and urban areas, many have adapted to preying on small birds at bird-feeding stations, launching from low tree branches rather than from a soaring flight. This same technique has been observed when taking koi. Good protection can be afforded by stringing nylon monofilament lines 18–24" (46–61 cm) apart across the pond. Although rather unsightly when strung near the pond surface, this method provides excellent protection against the herons and hawks. Of the group of fishing birds, cormorants (Phalacrocorax spp.) have been reported to have visited koi ponds and take koi. As they normally swallow fish whole, they will usually prey on only smaller koi, but injuries to larger koi are possible also. The belted kingfisher (Megaceryle alcyon) is a small diving bird whose feeding behavior is nearly impossible to mitigate. Fortunately, they will only dive and catch very small koi fry, so have not presented a major problem except for breeders using ponds. Again, removal of very small koi to a protected environment for growout is the best solution.

Last, but not least, is the newest emerging predator of koi, the osprey (Pandion haliaetus). Greatly threatened by habitat pollution, this protected species has been restored very successfully by elimination of DDT from the environment and the provision of a plethora of new nest sites across much of the US. As the population swelled, young birds have moved inland and adapted their feeding to koi ponds. Rather than high altitude dives, they are perching on nearby branches and attacking much like the hawks. However, unlike the hawks, being well suited to fish as prey, they can easily dive below the surface and take off from the water with koi of up to 2 lb (~ 1 kg) bodyweight. The only effective prevention has been with nylon monofilament lines strung over the pond surface. In well-designed koi ponds, where heron predation is not a concern, these lines can be strung overhead. When viewed from below, they are relatively invisible.