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The association between elevation (agro-climatic zones, ACZs) and the mean annual total rainfall (MATRF) is not straightforward in different parts of the world. This study sought to estimate the amount of MATRF across four elevation zones of Jema watershed, which is situated in the northwestern highlands of Ethiopia, by employing an appropriate interpolation method. The elevation of the watershed ranges from 1895 to 3518 m a.s.l. For the sake of this study, 34 sample MATRF data were extracted from satellite and nearby gauge stations that were recorded from 1983 to 2010. These data sources were reconstructed by International Research Institute for Climate and Society at Columbia University, USA, at a scale of 10 km by 10 km. An elevation data set generated from a digital elevation model with 30-m resolution (DEM 30 m) was considered as a covariable to estimate the MATRF. To identify the optimal interpolation model, mean errors were computed using cross-validation statistics. The root-mean-square error (RMSE) analysis showed that ordinary cokriging (OCK) was the most accurate model with a predictive power of 87.3%. The root-mean-square standardized (RMSSE) analysis showed that the best precision value (0.72) occurred in OCK. Stable and Gaussian trend lines together with local polynomial types of trend removal, and an elliptical neighborhood search function could perform best to maximize the accuracy and the precision of estimating MATRF. Elevation, as a covariable, enhanced the degree of accuracy and precision of estimation. The value of the trend line function (least square) between the MATRF and elevation was very weak (R2 = 0.07), whereas the value of trend line function (least square) between the MATRF and the longitude coordinates (east–west direction) was medium (R2 = 0.34). The estimated MATRF for the entire watershed under study ranged from 1228 to 1640 mm. To conclude, elevation could contribute to the estimation of the MATRF. The value of the MATRF showed a declining pattern from the lower to higher elevation areas of the watershed.