The Colombian Biogeographic Choco (CBC) and the La Plata Basin (LPB) are regions with high biodiversity. However, these areas are characterized by scarce climatological information, complex orography, and rain-gauge network unevenly distributed. Interpolated data from the ground station might overcome these aspects. For this reason, is necessary to identify the best technique for the spatial interpolation of rainfall. Hence, the spatial interpolation techniques were applied to annual and seasonal rainfall in the CBC and LPB. Geostatistical results and deterministic approaches were compared by cross-validation. Cokriging with spherical (gaussian) model is the best interpolator in the CBC (LPB), as indicated by the lowest root mean square error (RMSE) and a standardized RMSE close to one. The CBC shows three rainfall cores: the northern, 9,000 mm/year; the central-southern, 10,000 mm/year; and the southern, 7,000 mm/year. The LPB shows a west-east rainfall gradient, with a minimum to the west (450 mm/year) and a maximum in the mid-west (2,000 mm/year). To the north of the LPB, rainfall reaches 1,500 mm/year, while in the south it reaches only 900 mm/year. The results in our study may be useful for scientists and decision-makers for use in environmental and hydrological models for the CBC and the LPB.