Composting is a manure handling technique that has shown potential for small equine operations. It has been reported to provide many benefits including significantly reducing mass while producing a material that will deliver higher concentrations of plant available nutrients to fields than conventional manure spreading. This investigation was conducted to evaluate the impacts of three composting methods on the physical and chemical properties of equine stall waste and the water quality of stormwater runoff. The three methods include: (1) a static control pile, (2) a pile that was periodically turned, and (3) a covered pile that was periodically turned. The greatest pile mass reduction was observed in the covered treatment (43%) as compared to the turned treatment (38%) and lowest in the static pile (17%). The covered composting treatment also resulted in a material with significantly higher concentrations of available plant nutrients including total kjeldahl nitrogen, nitrate nitrogen, phosphorus and potassium, and significantly lower runoff concentrations of phosphorus than either the turned system or the static pile. This study provides evidence that a highly managed composting system can provide significant reductions in equine stall waste volume while reducing the potential for nutrient load and contamination of receiving waters.