The main recharge sources of the Yazd-Ardakan plain in central Iran with a desert climate is scarce rainfall events with an average amount of about 50 mm per year. The current study is the first attempt to systematically delineate the spatio-temporal variations in the isotopic composition of precipitation in this area. The isotopic value of the precipitation has little fluctuations during the rainy months of the year (November to April) with higher values in spring and lower values in winter at all sites. The Yazd-Ardakan meteoric water line was established as 62H = 4.45(+/- 0.05) x 618O - 7.45(+/- 0.3) (R2 = 0.92, N = 47), with a lower slope and intercept than the global meteoric water line, indicating deviations in humidity at the source of moisture or subcloud raindrop evaporation in the area with a desert environment. Air temperature is one of the most important factors controlling the isotopic composition of the precipitation in the desert area of Yazd-Ardakan plain. In most of the rainy events, the amount of precipitation was lower than 10 mm. Hence, the reverse effect of precipitation amount appears slightly occulted in the area by the combined effects of other climatic factors, such as temperature, moisture origin, and trajectory of the precipitating air masses. The altitude effect is about -0.79 parts per thousand/100 m for 618O, revealing the Rayleigh distillation model of air mass depletion. The large rainfall events totally displayed the highest slope, intercept, and d-excess values nearly similar to the snowfall samples, indicating the re-evaporation effects on the low rainfall amounts. Based on the d-excess values, air humidity sources in the study area can originate from the Mediterranean Sea, the Red Sea, and the Persian Gulf. Mediterranean Sea is the main moisture origin for the precipitation in the winter and to a lesser extent in the spring season, which is confirmed by trajectory analysis results by HYSPLIT modeling.