Nowadays, needs for renewable resources such as soil and water are increased due to growth in human opulation. However, ecosystem is becoming powerless to retain such important resources. Owing to this matter, to study and prognosticate the indicators of destruction and restoration of watersheds, including Karkheh as one of the biggest rivers in Iran is important. Modeling water resources can help in this regard, but the lack of data is a major problem in modeling water resources Karkheh River Basin. In this study, the SWAT2009 model (Soil and Water Assessment Tool) is used as an efficient tool in an area of 51,527 square kilometers in Karkheh basin to simulate runoff and sediment. For this purpose, we used three different climate data from various resources to predict runoff including: (1) Iranian Meteorological Organization climate data, (2) Iranian Ministry of Energy climate data, (3) Climate Research Unit climate data (CRU); and also a combined project of two groups of Iranian Meteorological Organization and CRU data.We considered the study period from 1995 to 2009 for Iranian Meteorological Organization data, 1995 to 2008 for Ministry of Energy data, and 1995 to 2006 for In three stations (Payepol, Hamidie, and abdolkhan), the determination coefficient in 4 runoff simulation models were almost identical and above 30 percent. At these stations, since starting the dam Inundation (2000) until the operation time (2002), in 4 of the runoff simulation models, no clear trend between flow simulation was observed. This shows the management in the area that outflow exits from the dam adjustably. This study tries to introduce the most appropriate input meteorological data for predicting runoff and sediment in Karkheh river basin. The results show that the SWAT2009 model designed with meteorology climate data simulated the flow and sediment runoff in the study area in a better way. For the three data groups the model was able to simulate runoff much better than sediment. According to the findings, the use of CRU data combined with meteorological data was considered relevant to simulate the runoff. Keywords: SWAT, climate data, Karkheh river basin, HRU, runoff, sediment