Pesticides are toxic chemicals used to control pests, weeds and pathogens. Three quarters of all pesticides are employed in agricultural production, particularly in developed countries, in an effort to mitigate crop damage endured by intensive agriculture. However, after more than 60 years of worldwide usage, their side-effects on terrestrial ecosystems – even when applied as recommended – are obvious. This chapter examines the ecological problems caused by specific chemicals/groups, so that this awareness may help improve agricultural practices through appropriate risk management. Fungicides alter the microbial-fungi communities responsible for the recycling of nutrients in the soil, and copper fungicides are toxic to earthworms and other animals. The routine application of herbicides has produced a net loss of plant biomass and biodiversity in many landscapes, which indirectly reduces the associated arthropod communities and leads to population declines in many species of birds, and possibly amphibians too, due to lack of food. Insecticides are very toxic to most invertebrates in the soil, birds and small mammals, causing significant reductions in their populations and disturbing the trophic structure of their communities. Persistent pesticides accumulate in soil and concentrate through the trophic chain, causing a plethora of sublethal effects which are negative for the survival of individuals as well as the viability of their populations; the long term effects of DDT and cyclodiene poisoning in birds is still an ecological issue despite more than 30 years of not being applied in most developed countries. While pesticides have increased our agricultural productivity and helped feed the current human population, the price of this productivity is being paid by the Earth's ecosystems at large.