S.D. Codified Laws § 46A-10A-30
Any board or commission under the provisions of this chapter and chapter 46A-11 may adopt a permit system for drainage. The permit system shall be prospective in nature. Permits shall be granted consistent with the principles outlined in § 46A-10A-20. The fee for a permit shall be established by the permitting authority, based on the administrative costs of regulating drainage activities, may not exceed one hundred dollars, and shall be paid only once. However, permitted drainage that is enlarged, rerouted, or otherwise modified requires a new permit. Any vested drainage right not recorded under the provisions of § 46A-10A-31 requires a permit for its use if a permit system has been established in the county where it exists. Any person or the person's contractor draining water without a permit, if a permit is required under the provisions of this section, is guilty of a Class 1 misdemeanor. In addition to or in lieu of any criminal penalty, a court may assess against any person violating the provisions of this section a civil penalty not to exceed one thousand dollars per each day of violation. A permit system is an official control.
SDCL 46A-10A-30