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Almeria (Spain) is one of the most important agricultural areas in Southern Europe, and pepper (Capsicum annuum L.) is one of the main crops produced under intensive conditions using fertigation. The lack of good quality irrigation water in this semi-arid area is an ever increasing problem. Experiments to evaluate the usefulness and the potential risks of using disinfected urban wastewater to fertigate pepper in a greenhouse were conducted. The aim of this study is to evaluate the potential soil and leachate pollution, and to compare the yield and fruit quality of pepper. Fertigation solutions were designed with good quality ground water and disinfected waste water. The pollutants Al, Cr, Ni, As, Cd, Sn, Sb, Hg, Pb, Co and micronutrients (Mn, Cu, Zn) were analyzed in soils after digestion in microwaves with HNO3-HCl by ICP-MS. In the leachates collected in lysimeters Al, Cr, Ni, As, Cd, Sn, Sb, Hg, Pb, Co, Na, nutrients (K, Ca, Mg, P, B, Mn, Cu, Zn, Mo) by ICP-MS and polycyclic aromatic hydrocarbons (PAHs) by using GC-MS, were analyzed. Results show that levels of pollutants and micronutrients do not differ between soil fertigated with disinfected wastewater and ground water. Leachates show no differences between disinfected wastewater and ground water with respect to inorganic pollution, and the levels of PAHs are lower than levels considered dangerous. Production, biomass and quality indices show the absence of significant differences between plants and fruits produced with good quality water and those obtained by fertigation with disinfected wastewater.