The use of pesticides has had one of the greatest negative effects on pollinator populations. Agricultural use of pesticides can lead to unintentional poisonings and to destruction of pollinator food sources. The use of pesticides can also lead to "chemical fragmentation," leaving a pollinator stranded in a pesticide-free area but unable to use the sprayed area for forage or travel.

When a pesticide is applied, pollinators foraging during the time or soon after, are poisoned through direct absorption, drinking tainted nectar, or gathering pollen covered in pesticide. Low doses of pesticides also have negative effects. Bees that have been exposed to low doses of pesticides have been seen exhibiting agitated or aggressive behavior and may have difficulty navigating or flying. Additionally, exposure to pesticides may have negative impacts on egg laying. Often times deaths due to pesticide application can be avoided or minimized by following the label application directions and recommendations (Reference: The Minnesota Honey Bee Battle In Pesticides and You, Spring 2006).