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Some pesticides used in crop protection have been found to be toxic to non-target species, for example animals. There are examples of chemicals, such as DDT, that persist in the environment and accumulate over time. This is called bioaccumulation and involves the build-up of a chemical in an organism. An increase in the concentration of a chemical such as DDT moving between the trophic levels of a food chain is known as biomagnification.

This may lead to poisoning of animals further along the food chain. Another problem with chemical control is that their use can lead to selective pressure that produces a resistant population of pests.

How and when chemical control is used can have an impact on its effectiveness and its cost. For example, the use of disease forecasts can suggest to farmers that they apply a fungicide as a preventative measure. This is far more effective than treating a diseased crop.