Water quality in agricultural watersheds is under greater scrutiny as hydrologic pathways are altered to increase the production of affordable food. Fertilizers are widely used in these watersheds to obtain desirable levels of nitrogen and phosphorus for optimal crop growth. Some of these nutrients are transported from the field to natural channel systems. Agricultural drainage ditches often provide an important pathway in this movement of nutrients. Ditches have been traditionally designed to remove water from agricultural lands. Little attention has been placed on alternative designs that are inherently more stable, assimilate nutrients and provide healthy ecosystems. In 2009, 2000m of a conventional drainage ditch in southern Minnesota was converted to an alternative drainage system with a two-stage channel, a rock trench, a rock inlet, and two linear treatment systems. These features not only increase ditch stability but also provide storage and attenuate sediment and excess nutrients. This paper discusses the design and construction of this alternative drainage system.