Salinity in soil and irrigation water is a major environmental stress in arid and semi-arid regions affecting soil organic carbon and its pools. A pot experiment was carried out in India to investigate distribution of soil carbon and its dynamic pools and nutrients under saline water irrigation in seed spice crops. Soil samples were analyzed for physicochemical properties (pH(1:2), EC1:2), soil carbon (inorganic and organic), its pools (vey labile, labile, less labile and non-labile), and soil nutrients. Soil pH and EC varied between 7.70-8.72 and 0.45-8.25 dS m(-1), respectively. Soil organic carbon and total soil carbon were higher by 15.2 and 22.4% with alternate application of saline and fresh water compared with continuous application of saline or fresh water and increased the less labile and non-labile carbon pools. Alternate application of saline and fresh water increased both the active and passive pools of carbon. Calcium carbonate and inorganic carbon were decreased by 35% with the continuous application of saline and fresh water. Similarly, alternate application of saline and fresh water increased carbon stock, carbon management index, and carbon pool index compared with sole application of fresh or saline water. Available nitrogen, phosphorous, and potassium varied from 310 to 629 kg ha(-1), 39 to 87 kg ha(-1), and 87 to 430 kg ha(-1), respectively. Micronutrients were found to be highest with alternate application of saline and fresh water. Zinc, iron, manganese, and copper varied from 2.66 to 5.24, 2.64 to 6.67, 4.60 to 13.07, and 1.36 to 3.66 mg kg(-1) soil, respectively. Alternate application of saline and fresh water helps in the build-up of soil carbon while maintaining the soil nutrient pools compared to sole application of saline or fresh water application.