Agro-ecosystems play a pivotal role in global food production and environmental sustainability. However, they are increasingly under threat from a variety of pollutants, both traditional and emerging, that impact soil and water quality, crop health, and human well-being. Selenium (Se), a naturally occurring trace element, is essential in small amounts but becomes toxic when concentrations exceed certain thresholds. In recent years, its interaction with emerging pollutants such as pesticides, heavy metals, pharmaceuticals, and microplastics has raised concerns about synergistic or antagonistic effects in agro-ecosystems. This chapter focuses on understanding the interactions between selenium and emerging pollutants, with an emphasis on their environmental fate, ecological impact, and potential consequences for agricultural sustainability and human health.