With the advent of the green revolution, fertilizers have become important to crop production. The conventional fertilizers have low nutrient use efficacy, nutrient losses, and degrading soil quality, while nanofertilizers ensure nutrient absorption and improve crop quality. Lack of standardization in formulation of nanofertilizers produces toxic wastes which causes soil and aquatic environment pollution. Therefore, nanofertilizers require safe handling as they carry respiratory disorders and carcinogenic effects on human health. The nanofertilizers could have unique biological and toxicological effects. There are concerns about nanofertilizers that these inhaled or entered human body via other routes, which may lead to health issues; their small size carries ability to penetrate through biological barriers. The nanofertilizers via food chain pose a potential threat to human health through the consumption of contaminated food, but their long-term health effects have not yet been explored. The nanofertilizers could impact the dynamics of ecosystem by affecting the soil and water quality, which again indirectly impact human health. To comprehend the risks of nanofertilizers, it is utmost important to ensure the safe use of nanofertilizers and to develop regulatory frame work.