This research aims at assessing the impact of drought (in the form of original and modified reconnaissance drought indices (ORDI and MRDI)) on water productivity of rainfed winter wheat in some arid and semi-arid regions of Iran. It focuses on different timescales of drought to determine which period of the year had the greatest significant impact. RDI was modified using the Food and Agriculture Organization of the United Nation method (FAO) (MRDI-1), US Bureau of Reclamation (USBR) (MRDI-2), the Simplified version of Soil Conservation Service of the US Department of Agriculture method (USDA-SCS-simplified) (MRDI-3), and the CROPWAT version of USDA-SCS method (USDA-SCS CROPWAT) (MRDI-4). Results showed that in Tabriz and Zanjan stations, 3-month scale of MRDI-2; in Ghazvin, Arak, and Kerman stations, 6-month scale of MRDI-4; in Sanandaj station, 12-month timescale of MRDI-3; and in Shiraz stations, 1-month timescale of MRDI-1 resulted in the highest values of correlation coefficients. According to the goodness-of-fit parameters, in Tabriz and Zanjan stations, MRDI-1; in Ghazvin, Arak and Kerman stations, MRDI-2; in Shiraz station, MRDI-3; and in Sanandaj station, ORDI resulted in the best generalized estimating equation model. These results can be useful to plann for the management of cultivation in impressive timescales.