One way stormwater is regulated is through the National Pollutant Discharge Elimination System (NPDES).
See NPDES wiki
"NPDES only applies to “point sources” of water pollution, specifically a “discernable, confined, discrete conveyance” into waters of the United States (CWA section 502(14)). Point sources include direct effluent pipes and conduits, ditches, tunnels, and more. Stormwater is included as a point source of pollution, due to stormwater drain discharges, culverts, and other infrastructure that channel stormwater to a receiving surface water. Industrial sources and stormwater sources are regulated differently due to the reasonable control over pollutant input (e.g. direct effluent from a facility versus urban runoff), where stormwater permits are based more on “best management practices” rather than numeric water quality limits. There are also specific exemptions of industrial and stormwater point source pollution, and non-point sources of pollution like agricultural operations are not subject to NDPES permits."
While some places do treat stormwater, many times stormwater drains directly into waterways.