The main sources of soil contamination are anthropogenic activities, which result in the accumulation of contaminants that can reach levels considered toxic. One of the main soils contaminants these days is heavy metals. These metals are bioaccumulative and are not biodegradable, so many of them are toxic when they exceed certain limits. Heavy metals, when accumulated in the tissues of plants, animals and humans, induce severe symptoms that can even cause death. Bioremediation is a widely used technology to decrease the levels of these metals in soils and waters using microorganisms, among which fungi stand out. Nanotechnology currently applies the bases of bioremediation using fungi at the nanoparticle level to treat soils contaminated with heavy metals. This chapter will discuss novel aspects related to heavy metals in modern agriculture, bioremediation and nanotechnology using fungi with bioremediation purposes.