Impacts of cover crops, tillage and abiotic factors on soil nitrogen (N) dynamics, greenhouse gas emissions, and microbiological functions were investigated in a vineyard in California's Mediterranean climate. Treatments had been established in fall 2001 and were composed of two cover crops [Trios 102 ( Triticale × Triosecale), (‘Trios’), Merced Rye ( Secale cereale), (‘Rye’)] and cultivation (‘Cultivation’). Soils were sampled every 2–3 weeks from November 2005 to November 2006. Effects of season and treatment on potential nitrification and denitrification also were determined. Gravimetric water content (GWC) reflected winter and spring rainfall, and soil temperature generally did not differ among treatments. Microbial biomass N (MBN) typically was 2–3-fold greater in ‘Rye’ and ‘Trios’ than ‘Cultivation’ in winter and spring, but these differences among treatments disappeared in summer. Soil nitrate (NO 3 −–N) was consistently greater in cultivated soils, with little temporal change in any treatment. In contrast, soil ammonium (NH 4 +–N) in cover crop treatments was 2–3-fold greater than ‘Cultivation’ in winter and spring, increasing in all treatments in summer after cover crops had been mowed and ‘Cultivation’ had been tilled. Significant multiple linear regressions of MBN on GWC, soil temperature, NH 4 +–N and NO 3 −–N for all treatments indicated that GWC significantly explained changes in MBN. Soil temperature also was significant for ‘Trios’ only, but its standard coefficient value was low, indicating its lesser importance in determining MBN. Despite a significant multiple linear regression of nitrous oxide (N 2O) efflux on GWC, soil temperature, NH 4 +–N and NO 3 −–N in ‘Trios’ only, no single variate explained the observed variation. However, increases in N 2O were detected after both cultivation and increases in GWC from precipitation in winter, late spring, and fall. Mean daily N 2O efflux was greater in cover crops, but annual N 2O efflux was low as compared to fertilized and unfertilized annual cropping systems. Potential nitrification, N mineralization and denitrification were generally 2–4-fold greater in cover crop treatments than ‘Cultivation’. Thus, cover crops enhanced the soil's capacity for supporting greater MBN, potential N mineralization, and the microbiological functions of nitrification and denitrification. Also, N dynamics appear to be more sensitive to changes in soil water content than temperature. We suggest that potential impacts of greater N 2O emissions from cover crop soils be evaluated with reference to other benefits of cover cropping, such as increased soil organic matter content, improved microbiological activity, and N availability.