Soil is the major source that helps in agriculture, farming and regulates the discharge of excess rainwater, thereby preventing flooding. Nowadays by the growing population, many industries have emerged to meet people’s needs. Without a proper waste management system industrial effluents like toxic heavy metals, various types of dyes from the textile industry, and the use of pesticides in crops get accumulated in the soil. Unfortunately, soil is being contaminated as a result of improper industrial waste disposal. This eventually affects the littoral and sub-littoral regions nearby soil. By this aqueous water bodies were becoming contaminated with the harmful chemical substances that harm marine organisms. This can cause diseases and infectious conditions in plants and animals. When this is consumed by humans, it leads to food poisoning, digestive problems, respiratory and heart disease, sometimes in severe cases, even leads to death. As a result, the flora and fauna of the ecosystem were getting affected majorly. Agricultural soil contamination can be treated by soil bioremediation method. Soil bioremediation is the process that reduces the toxicity of heavy metals contaminated in soil and improves the quality of the soil. However, bioremediation itself is a sustainable approach to treating contaminated soil. Bioremediation is considered safe, sustainable, and cost-effective. In this chapter, we have performed a brief literature survey based on biological methods for the removal of organic waste by reducing its toxicity from agricultural soil with an understanding of the bioremediation of soil contaminants using microorganisms.