Keep in mind that nonpoint source water pollution (from diffuse runoff) is much different than point source pollution (usually thought of as the end of a discharge pipe) and each type is handled separately by the Clean Water Act. Nonpoint source can be from farm field runoff, storm water runoff, and the like. If you overapply fertilizer, etc. then it can lead to nonpoint source pollution. However, nothing under the federal law (various states have their own programs) requires doing anything as far as nonpoint source pollution unless a stream is found to be impaired for its designated uses; i.e. in Wyoming a cold water fishery can be impaired by sediment, temperature or other issues, a primary contact recreation water body can be impaired by e. coli, etc. If sediment is coming from diffuse runoff and causing the impairment, then a "total maximum daily load" (TMDL) is established and the landowners in the drainage are required to apply best management practices to reduce the load. The nonpoint source part of the CWA is generally voluntary, but the agency (usually the states have primacy with the EPA holding a stick behind them with the threat EPA will take over and a carrot out from of them in the form of funding and grants) can do some regulatory action to implement the water quality standard.
Point source pollution is handled with the National Pollutant Discharge Elimination System. All point sources such as water treatment plants, feedlots (Confined Animal Feeding Operations (CAFOs), factories, etc. have to have a permit to discharge. These permits are tightly regulated and subject to citizen suit provisions as well as large civil penalties for violation of the discharge limitations. The NPDES dischargers may have their allowable discharges reduced due to the background pollution caused by nonpoint source pollution. This is probably what this DesMoines water guy is referring to, but he needs to realize that there might not be much of a city if not for the ag and residential upstream of it.
The Section 404 dredge and fill part of the CWA is separately regulated from the nonpoint source program and the NPDES system, although dredge and fill is a point source activity.
To answer an earlier question, planting a fence post in a water of the U.S. or a wetland could be a discharge of a pollutant under the CWA and in violation of Section 404. However, Section 404(f)(1)(A) exempts normal agricultural activities from regulation. Refer to my earlier post about what EPA is attempting to do by narrowing the range of exempt ag activities to only NRCS approved practices.