The Sustainable Agricultural Farming Systems project began at UC Davis in 1988 to examine the transition from conventional to sustainable and organic systems. The conventional system received normal inputs of fertilizers and pesticides. The sustainable systems received about half of the conventional fertilizer and nitrogen, and were supplemented with legume winter cover crops. The organic system received composted manure at 8 tons wet weight per hectare and winter cover crops as sole nitrogen sources. The winter cover crops required additional cutting and incorporation compared to the conventional system. After five years, the organic treatment sequestered 5 tons of soil carbon per hectare and the sustainable system sequestered 3 tons of carbon per hectare. The difference of 2 tons carbon in the organic system compared to the sustainable system was the result of the manure addition. After 10 years, no new soil carbon was sequestered in the organic or sustainable system, showing that the soil had reached equilibrium after 5 years. In addition, to maintain the soil carbon management with cover crops and manure would be required indefinitely. These results suggest that the carbon sequestration value in soil is limited and the amount depends on the intensity and consistency of inputs. The increased soil carbon in the organic and sustainable systems resulted in increased water infiltration and storage of winter rain and resulted in a positive water balance compared to the conventional system. The organic and sustainable system lost less than 5% of their added nitrogen inputs compared to the conventional system, which lost 30%. The smaller losses resulted in significantly less nitrate leaching and nitrous oxide losses in the organic and sustainable systems. This study shows the value of adding sustainable practices to enhance soil properties to reduce water losses and retain more carbon and nitrogen.