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Established populations of plants, insects and other species with dormant life stages (eg. soil seedbanks) and high intrinsic rates of increase present more of a challenge for eradication, even in isolated populations. Typically, the eradication of plant populations involves a long campaign, involving the sustained removal of individuals before they set seed. In the longer term these species will be just as damaging to ecosystems as the more rapid and visible impact of many mammals.

In many situations, the feasibility of eradication will also be affected by risks to non-target species. This may prevent the use of certain techniques and limit the use of others. In some situations the risks to non-target species (including livestock, pets, crops and people) currently precludes the attempted eradication of some invasive species. However, some non-target deaths are acceptable if eradication of the invasive species is achieved and recovery of the affected non-target species is likely to be rapid. For example, in the course of the eradication of brushtail possums (Trichosurus vulpecula) from Kapiti Island, New Zealand, 181 birds were killed in traps, 39% of which were kereru (Hemiphaga novaeseelandiae)(Cowan 1992). Following the possum eradication (and subsequent eradication of rats by poisoning), the forest recovered substantially and kereru abundance rose up to six fold (Veltman 2000).