The agricultural industry uses substantial amounts of water (the highest in the world) mostly for irrigation purposes. Rapid population growth and, consequently, growing demand for food have increased the use of pesticide to have higher yield for crops and other agricultural products. Wastewater generated as a result of excessive use of pesticides/herbicides in agricultural industry is becoming a global issue specifically in developing countries. Over 4,000,000 tons of pesticides are currently used in the world annually and high concentrations above their threshold limits have been detected in water bodies worldwide. The generated wastewater (contaminated with pesticides) has negative impacts on human health, the ecosystem, and the aquatic environment. Recently, biodegradable and biocompatible (including plant-based) pesticides have been introduced as green and safe products to reduce/eliminate the negative impacts of synthetic pesticides. Despite positive advantages of biopesticides, their use is limited due to cost and slow interaction with pests compared to chemical pesticides. Pesticides may also react with water and constituents of soil resulting in formation of intermediates having different physical and chemical properties. Diffusion, dispersion, and permeation are main mechanisms for transfer of pesticides in soil and water. Pesticides may degrade naturally in nature; however, the time requirement can be very long. Many mathematical models have been developed to simulate and estimate the final fate of pesticides in water resources. Development of new technologies and environmentally friendly pesticides to reduce water contamination is becoming increasingly important.