First of all, let's clarify the terms: when you say pesticides it refers to chemicals, either natural or artificially made, that control any form of pests infesting plants. Herbicides refer to chemicals, natural or artificially made, that control plants considered as weeds. Please note that a herbicide is one form of pesticide.
The pesticides obtained from natural origins, e.g. extracts from plants that have a pesticidal effect, usually are biodegraded and have minimum or almost no negative effect on the environment. On the other hand, artificial pesticides, e.g. those made by man, tend to have a harder time degrading into much simpler molecules hence they tend to pollute the environment in the long run.