Can all agriculturally productive soils store an unlimited amount of carbon if we “just use regenerative agriculture practices?” Do tillage and cover cropping increase soil carbon in high-value annual cropping systems California’s mediterranean climate? Does the production of dairy manure compost result in nitrate leaching? Can nitrate be attenuated through natural processes present in some soils? This dissertation addresses these questions that the author tackled during his doctoral research at UC Davis. State agency funding made this research possible through: 1) A California Department of Food and Agriculture (CDFA) – Healthy Soils Program (HSP) – Demonstration Project – Type A and B and 2) A California Department of Water Resources (CDWR) – Funded Project – ‘Dairy Manure Composting in California’. The main findings of his work are in the following pages, but the main theses follow. Much of the existing research on cover cropping and no-till, suggests that no-till increases soil carbon. My data takes that into question and does not support the positive correlation of no-tillage, alone or combined with cover cropping, to organic carbon accumulation in the top 90 cm of soil in the semi-arid to arid mediterranean climate of California. Second, given the reductive effect sub-surface irrigation has already had on nitrous oxide emissions, there does not appear to be a further substantive effect, lowering emissions as a result of no-tillage or cover cropping. There is an excess of dairy manure and the nitrogen and phosphorus it contains can be harmful to the environment if allowed to enter groundwater. Composting has been suggested as an improvement on existing practices which often include static piling. But questions remain about whether composting likely to result in nitrate leaching into groundwater. My research shows that nitrate is produced by composting. However, I also found that soil conditions found in the subsurface attenuated this leached nitrate to background levels through denitrification. I posit that the same would be true at many sites with heterogeneous soil textures including subsurface clay layers. These findings do align with much of the published work on the mechanisms driving denitrification but have not been demonstrated in this way before. The above findings add to the great body of research in Soils and Biogeochemical processes and summarize a great deal of the research I accomplished during my tenure as a graduate student at UC Davis.