Microbial biomass carbon (MBC), a small fraction of soil organic matter, has a rapid turnover rate and is a reservoir of labile nutrients. The water-extractable carbon pools provide a fairly good estimate of labile C present in soil and can be easily quantified. Changes in soil MBC and water-extractable organic carbon pools were studied in a 14-year long-term experiment in plots of rice-wheat rotation irrigated with canal water (CW), sodic water (SW, 10-12.5 mmol c L-1 residual sodium carbonate), and SW amended with gypsum with or without application of organic amendments including farmyard manure (FYM), green manure (GM), and wheat straw (WS). Irrigation with SW increased soil exchangeable sodium percentage by more than 13 times compared to irrigation with CW. Sodic water irrigation significantly decreased hot water-extractable organic carbon (HWOC) from 330 to 286 mg kg-1 soil and cold water-extractable organic carbon (CWOC) from 53 to 22 mg kg-1 soil in the top 0-7.5 cm soil layer. In the lower soil layer (7.5-15 cm), reduction in HWOC was not significant. Application of gypsum alone resulted in a decrease in HWOC in the SW plots, whereas an increase was recorded in the SW plots with application of both gypsum and organic amendments in both the soil layers. Nevertheless, application of gypsum and organic amendments increased the mean CWOC as compared with application of gypsum alone. CWOC was significantly correlated with MBC but did not truly reflect the changes in MBC in the treatments with gypsum and organic amendments applied. For the treatments without organic amendments, HWOC was negatively correlated with MBC (r = 0.57*) in the 0-7.5 cm soil layer, whereas for the treatments with organic amendments, both were positively correlated. Irrigation with SW significantly reduced the rice yield by 3 t ha-1 and the yield of rice and wheat by 5 t ha-1 as compared to irrigation with canal water. Application of amendments significantly increased rice and wheat yields. Both the rice yield and the yield of rice and wheat were significantly correlated with MBC (r = 0.49**-0.56**, n = 60). HWOC did not exhibit any relation with the crop yields under the treatments without organic amendments; however, CWOC showed a positive but weak correlation with the crop yields. Therefore, we found that under sodic water irrigation, HWOC or CWOC in the soils was not related to MBC. Microbial biomass carbon (MBC), a small fraction of soil organic matter, has a rapid turnover rate and is a reservoir of labile nutrients. The water-extractable carbon pools provide a fairly good estimate of labile C present in soil and can be easily quantified . Changes in soil MBC and water-extractable organic carbon pools were studied in a 14-year long-term experiment in plots of rice-wheat rotation irrigated with canal water (CW), sodic water (SW, 10-12.5 mmol c L- 1 residual sodium carbonate), and SW amended with gypsum with or without application of organic amendments including farmyard manure (FYM), green manure (GM), and wheat straw (WS). Irrigation with SW increased soil exchangeable sodium percentage by more than 13 times compared to irrigation with CW. Sodic water irrigation significantly decreased hot water-extractable organic carbon (HWOC) from 330 to 286 mg kg -1 soil and cold water-extractable organic carbon (CWOC) from 53 to 22 mg kg -1 soil in the top 0-7.5 cm soil layer. In the lower soil layer (7.5-15 cm), reduction in HWOC was not significant. Application of gypsum alone resulted in a decrease in HWOC in the SW plots, an an increase was recorded in the SW plots with application of both gypsum and organic Nevertheless, the application of gypsum and organic amendments increased the mean CWOC was compared with application of gypsum alone. CWOC was significantly correlated with MBC but did not candidly reflect the changes in MBC in the treatments with gypsum and organic amendments applied. For the treatments without organic amendments, HWOC was negatively correlated with MBC (r = 0.57 *) in the 0-7.5 cm soil layer, for for treatments with organic amendments, both were positively correlated. Irrigation with SW significantly reduced the rice yield by 3 t ha-1 and the yield of rice and wheat by 5 t ha-1 as compared to irrigation with canal water.Both the rice yield and the yield of rice and wheat were significantly correlated with MBC (r = 0.49 ** - 0.56 **, n = 60). HWOC did not exhibit any relation with the crop yield under the treatments without organic amendments; however CWOC showed a positive but weak correlation with the crop yields. Therefore, we found that under sodic water irrigation, HWOC or CWOC in the soils was not related to MBC.