Selenium (Se) is a trace element essential for plant and animal nutrition, but its availability and toxicity in the water-soil–plant environment are complex and context-dependent. This chapter explores the dynamics of selenium across these interconnected systems, focusing on its biogeochemical behaviour, speciation, bioavailability, and the factors influencing its distribution. The interactions between selenium and soil properties, irrigation practices, and plant uptake mechanisms are examined, alongside the roles of microorganisms in selenium transformation. Special attention is given to selenium’s dual nature, balancing deficiency and toxicity, and the implications for agriculture, environmental sustainability, and human health. Case studies illustrate the challenges and opportunities selenium management presents in different agroecosystems. Strategies for optimising selenium bioavailability in crops, including selenium fertilisation and phytoremediation, are also discussed, providing insights into sustainable agricultural practices that can mitigate the risks of both selenium deficiency and excess.