Irrigation runoff and tailwater conveyance systems which are in direct hydrologic communication with a water of the U.S. should be subject to Clean Water Act authorities. A lake most certainly is a navigable waterbody, hence a WOTUS.
Here is where the problem comes in: when the Clean Water Act was crafted and adopted in 1972, the agricultural industry convinced congress to exempt agriculture from the legal accountability with the requirements of the Clean Water Act, at least from the water quality angle. Hydromodification I think is separate issue. Drafts of the law did not exempt agriculture from water quality compliance, so there was obviously a sustained lobbying effort to get agriculture off the hook. The only way Clean Water Act addresses agriculture is through voluntary compliance and giving them NPS grants for watershed improvement efforts.
That's where state authorities have to come into play, IMO. Since agriculture is largely off the hook from the water quality perspective under the CWA framework, the only tangible option at this point is to have states adopt enforceable requirements for agriculture to protect water quality.
