Glucosinolates are a class of phytochemicals produced by most species of the family Brassicaceae. Because their breakdown products (mustard oils) deter feeding by many insects, they are most commonly known as anti-herbivory defensive chemicals. Much of the variation in glucosinolate profiles across Brassicaceae has a genetic basis, or is induced upon herbivore or pathogen attack. Recent work, however, suggests that glucosinolates' roles in plant ecology and evolution are more complex than previously appreciated. Here we describe our observations of the wild perennial crucifer, Boechera stricta, which harbors natural polymorphism at a major-effect locus controlling glucosinolate production. Years of large-scale field and greenhouse experiments demonstrate that herbivores are not the only ecological factor driving natural selection on this trait: water availability is also a key constraint on glucosinolate evolution. Furthermore, accumulating evidence from multiple species indicates that glucosinolates alter not only susceptibility to pathogens, but also mutualist and commensal microbes, particularly belowground. Finally, we discovered that variation in soil properties among natural B. stricta habitats has surprisingly strong effects on constitutive glucosinolate content in both leaves and roots. In summary, glucosinolate variation in B. stricta has many causes and many ecological consequences that affect its evolution across the complex landscapes of western North America.