The discipline of chemistry has made agricultural chemicals, such as fertilizer and pesticides, available to society.

which is a negative effect of these chemicals on society?

In the case of fertilizer, runoff containing the chemicals intended to increase plant growth can reach rivers, **lakes, and oceans, where it can cause massive algae blooms that bloom quickly and then die quickly, leaving the region full of decaying organic material that causes hypoxic water conditions, killing many other plants and animals. 
Pesticides negatively effect insects, as intended, but they can also unintentionally harm wildlife, as pesticides are intended to be toxic enough to eliminate living organisms. Additionally, while I do not have the appropriate scientific journal on my laptop, regions of high pesticide use has been found in various human tissue and fluid samples of those living there, leading some scientists to say that the pests being eradicated aren't worth the risk to human health.