A complete solar energy system was designed and constructed in the workshop of Agricultural Engineering Department. It was installed on the roof of the department at altitude angle of 31.045 °N in order to collect, store, and utilize the solar energy available in heat treatment process of greenhouse root-media mixture. The solar energy system was mainly consisted of three components: solar water heater has a surface area of 2.0 m² (2 x 1 m), insulated storage tank (332 litres), and heat distributing system (heat exchanger) using parallel flow system. Water was continually pumped between the insulated storage tank and the solar water heater during daylight time. The container of heat treatment was equipped by a heat exchanger and filled up by 0.6 m³ of greenhouse root-media. In order to catch and hold more heat energy and reduce the heat losses, the upper surface of root-media container was covered with polyethylene sheet. After sunset of each day (six and five successive days were recorded during the two experiments) the hot water (heated by solar heating system) was pumped between the insulated storage tank and the heat distributing system (heat exchanger) inside the container of root-media. Solarization technique in heat treatment of root-media was also functioned after fulfilled the heat treatment process was. Two mathematical models were developed and used to compute the water and soil-based root-media temperatures according to the heat energy balance on the storage tank and root-media heat treatment unit, respectively. The total microbial contamination of root-media samples were bacteriological analysed before and after the heat treatment process. The obtained data revealed that, the daily average overall thermal efficiency of the solar water heater during these experiments was 71.99%, consequently 28.01% of the total solar energy available was lost. The daily average solar energy stored in the storage tank during the experimental work was 12.807 kWh/day, which gave an average storage system efficiency of 82.99%. The predicted water temperatures in the storage tank were validated very well with that measured by 98.61 % which gave an excellent agreement. The predicted root-media mixture temperatures in the heat treatment unit were validated very well with that measured by 99.65% which gave an excellent agreement. The daily average effectiveness of heat distributing system during the experimental work was 76.09%. Due to use the solar heating system in root-media heat treatment process, there were no any weeds observed in all pots of the plants, the E.coli microbial content on average reduced from 5.311 x 10³ to 8.1154 x 10^-³ CFU/g, and the Salmonella organisms on average reduced from 3.20 x 10³ to 100 CFU/g. The technique of solarization for heat manipulating of root-media led to destroy the remained of microbial organisms in the root-media.