For centuries, wastewater has been improperly used in agriculture, presenting potential risks to public health and the environment. In the context of scientific development, and confronted by an increasing water crisis, wastewater reuse merits consideration because the practice helps decrease water use pressure and moderates water pollution. Thus, this article presents a literature review that addresses the effects, both positive and negative, of wastewater use in agriculture, emphasizing the effects on the soil environment. The literature review reveals that, until the 1990s, research studies promoted the use of wastewater for irrigation purposes from a treatment approach, while proposing “end of pipe” conventional solutions. However, more recent research studies (2012–2016) reveal that agricultural reuse significantly affects soil texture properties, while also causing possible alterations of the biomass and microbiota. In addition, research in this period has been oriented to the quantitative evaluation of microbiological risk.