The US Congress passed the Clean Water Act in 1972 to protect and restore America's waterbodies by regulating pollutant discharges from point sources such as industrial plants and sewer pipes. Over the years, Congress expanded the law to include non-point sources like polluted runoff from roads and agricultural areas. However, routine agriculture drainage maintenance activities, like continuously farmed wetlands and drainage ditch dredging, are exempted under the Clean Water Act. These exemptions allow sediment pollution to continue to be a major issue in agricultural streams and waterbodies managed by drainage districts. We examine the shortcomings of the Clean Water Act to address sediment pollution from the perspective of routine agricultural activities like drainage ditch maintenance and offer policy recommendations to mitigate its impacts. We discuss the exclusion of agricultural sediment originating from these activities as a major non-point pollution source under the Clean Water Act, the consequences of sediment pollution on aquatic ecosystems and stream water quality in agricultural streams, and the need for monitoring and regulation of sediment discharge from farming practices. In our analysis, we also consider the interaction between the state drainage laws and federal regulations. Finally, we seek to address gaps in the current regulatory structure and offer suggestions regarding better protection of water quality and ecosystem health in drainage districts.