Retrofitting stormwater systems with sensors and controllers will allow cities to be operated as real-time, distributed treatment plants. Unlike static infrastructure, which cannot adapt its operation to individual storms or changing land uses, “smart” stormwater systems will use system-level coordination to maximize watershed pollutant removal and treatment. We illustrate that this vision is not limited by technology, which has matured to the point at which it can be ubiquitously deployed. Rather, the challenge is much more fundamental and rooted in a system-level understanding of environmental science. Once distributed stormwater systems become highly instrumented and controlled, how should they be operated to achieve desired watershed outcomes? The answer to this question demands the development of a theoretical framework for smart stormwater systems. In this paper, we lay out the requirements for such a theory. Acknowledging that the adoption of these systems may still be years away, we also present a modeling framework to allow for the simulation of controlled stormwater systems before they become commonplace. We apply this control framework to two simulated case studies in which stormwater sites are controlled to reduce nitrate loads to downstream water bodies.