In recent years, there has been a steady increase in the quantity of agricultural waste generation, due to the increased production of the food supply chain and the production of fuel for greenhouse gas (GHG) emission reduction initiatives, viz. processing, and consumption. As a result, there have been a number of environmental concerns, such as waste disposal, governance, and environmental impact. Hence, repurposing such wastes into high-value goods such as silica nanoparticles (SNPs) has received a lot of scientific attention. Because of their controllable pore size, large surface areas, and tunable and tailorable structure, SNPs have attracted interest from scientists for a variety of applications. As the water resources are becoming scarce and heavily stressed, our ongoing efforts have been towards the green synthesis of nanoparticles, with an emphasis on mitigating waterborne contaminants. Recent advances in the synthesis of SNPs from barley and rice husk agricultural waste, as well as its use in the removal of several recent environmental pollutants from water, have attracted the attention of several researchers, including our group. By fine-tuning the processing parameters during synthesis, the characteristics of SNPs are altered in terms of their configuration, appearance, porosity, and dimensions. Such features and corresponding applications of the SNPs are being investigated in order to investigate whether agricultural waste may be utilized for silica precursors. Although the utilization of low-cost waste-derived minerals appears to have the potential for both waste reduction and the creation of value-added goods, further studies are needed to increase silica production, particularly on a commercial scale. In addition, we conducted a review of the efficacy of SNPs toward water contamination mitigation and our results of such investigation are reported here. It is observed that silica nanoparticles can be synthesized on a commercial scale using green chemistry principles and are highly efficient materials with promising outcomes for environmental applications. Hence, using green synthesis, we are able to reduce agricultural waste, while mitigating environmental contaminants using environmentally friendly processing.