Crop cultivation in Djibouti is mainly done by irrigation agriculture obtaining groundwater from wadi aquifer. The decreasing in the efficiency of solar power generation system due to panel-on-dust is reported to be the issue in terms of energy loss in pumping up water. In this paper, the effect of dust deposition for solar pumping system was evaluated at wadi agriculture farm in Dikhil, Djibouti. The amount of panel-on-dust was measured to be 1.88 and 2.1 g/m² in cooler season (dry deposition) and in hot season (wet deposition), respectively. Clearance of the panel-on-dust resulted a decline in the output power of photovoltaic panel due to the rise in panel surface temperature in January (cooler season), whilst the output power increased in September (hot season) when the panel surface temperature was relatively higher. The conversion efficiency of the photovoltaic power generation was calculated to be about 5 - 6% lower in September than in January. The whole conversion efficiency of solar pumping system was estimated to be about 2%. Since the ideal conversion efficiency was calculated as 6.76%, the gap from observed value of about 4.5% can be implied by suppressing water leakages from the system in pumping process.