It is commonly presumed that organic agriculture causes only minimal environmental pollution. In this study, we measured the quality of percolating water in the vadose zone, underlying both organic and conventional intensive greenhouses. Our study was conducted in newly established farms where the subsurface underlying the greenhouses has been monitored continuously from their establishment. Surprisingly, intensive organic agriculture relying on solid organic matter, such as composted manure that is implemented in the soil prior to planting as the sole fertilizer, resulted in significant down-leaching of nitrate through the vadose zone to the groundwater. On the other hand, similar intensive agriculture that implemented liquid fertilizer through drip irrigation, as commonly practiced in conventional agriculture, resulted in much lower rates of pollution of the vadose zone and groundwater. It has been shown that accurate fertilization methods that distribute the fertilizers through the irrigation system, according to plant demand, during the growing season dramatically reduce the potential for groundwater contamination from both organic and conventional greenhouses.