Cover crops may influence soil carbon (C) sequestration and microbial biomass and activities by providing additional residue C to soil. We examined the influence of legume [crimson clover (Trifolium incarnatum L.)], nonlegume [rye (Secale cereale L.)], blend [a mixture of legumes containing balansa clover (Trifolium michelianum Savi), hairy vetch (Vicia villosa Roth), and crimson clover], and rye + blend mixture cover crops on soil C fractions at the 0–150 mm depth from 2001 to 2003. Active fractions of soil C included potential C mineralization (PCM) and microbial biomass C (MBC) and slow fraction as soil organic C (SOC). Experiments were conducted in Dothan sandy loam (fine-loamy, kaolinitic, thermic, Plinthic Kandiudults) under dryland cotton (Gossypium hirsutum L.) in central Georgia and in Tifton loamy sand (fine-loamy, siliceous, thermic, Plinthic Kandiudults) under irrigated cotton in southern Georgia, USA. Both dryland and irrigated cotton were planted in strip tillage system where planting rows were tilled, thereby leaving the areas between rows untilled. Total aboveground cover crop and cotton C in dryland and irrigated conditions were 0.72–2.90 Mg C ha⁻¹ greater in rye + blend than in other cover crops in 2001 but was 1.15–2.24 Mg C ha⁻¹ greater in rye than in blend and rye + blend in 2002. In dryland cotton, PCM at 50–150 mm was greater in June 2001 and 2002 than in January 2003 but MBC at 0–150 mm was greater in January 2003 than in June 2001. In irrigated cotton, SOC at 0–150 mm was greater with rye + blend than with crimson clover and at 0–50 mm was greater in March than in December 2002. The PCM at 0–50 and 0–150 mm was greater with blend and crimson clover than with rye in April 2001 and was greater with crimson clover than with rye and rye + blend in March 2002. The MBC at 0–50 mm was greater with rye than with blend and crimson clover in April 2001 and was greater with rye, blend, and rye + blend than with crimson clover in March 2002. As a result, PCM decreased by 21–24 g CO₂–C ha⁻¹ d⁻¹ but MBC increased by 90–224 g CO₂–C ha⁻¹ d⁻¹ from June 2001 to January 2003 in dryland cotton. In irrigated cotton, SOC decreased by 0.1–1.1 kg C ha⁻¹ d⁻¹, and PCM decreased by 10 g CO₂–C ha⁻¹ d⁻¹ with rye to 79 g CO₂–C ha⁻¹ d⁻¹ with blend, but MBC increased by 13 g CO₂–C ha⁻¹ d⁻¹ with blend to 120 g CO₂–C ha⁻¹ d⁻¹ with crimson clover from April 2001 to December 2002. Soil active C fractions varied between seasons due to differences in temperature, water content, and substrate availability in dryland cotton, regardless of cover crops. In irrigated cotton, increase in crop C input with legume + nonlegume treatment increased soil C storage and microbial biomass but lower C/N ratio of legume cover crops increased C mineralization and microbial activities in the spring.