It’s common practice to cook beans in the same water they’re soaked in (if they’re soaked at all), says Lynne Bigwood, a home economist for the Northarvest Bean Growers Association, and it is particularly important to do so if you are cooking black beans. The black pigments in the skin are water soluble, so “if you want to retain as much color as possible, you need to preserve [it] by keeping the soak/cooking water around the bean until it is tender.”
Cooking beans in their soaking water will also yield a thicker broth, says Diana L. Caldwell, a spokesperson for the Idaho Bean Commission. However, if you’re bothered by “undesirable side effects” when you eat beans (that’s code for farting), you should drain and rinse them, and cook using fresh water, says Lynn Reuter, a spokesperson for the Nebraska Dry Bean Commission. “The soaking process breaks down the oligosaccharides, the indigestible sugars in beans that cause gas,” she explains. Draining the soaking liquids would reduce the indigestible sugars.