Owing to the shortage of good quality irrigation water all over the world for use in agriculture, disinfected wastewater could be a well-priced stable source. Because of poor control of wastewater quality, pollutant accumulation and relevant ecotoxicological effects may occur, especially for inorganic pollutants (heavy metals), organic pollutants (pesticides and other persistent compounds) and human pathogenic organisms. In our study, urban wastewater from the town of Almeria (Spain), after primary and secondary treatments in the wastewater treatment plant, was pumped to a tertiary treatment plant. Wastewater samples were taken before tertiary treatment, after chlorination and after chlorination plus ozonization. This paper reports on the effect of the disinfection systems on the content of inorganic pollutants (Al, Cr, Co, Ni, As, Se, Cd, Sb, Hg, Pb), polycyclic aromatic hydrocarbons (PAHs) and total and faecal coliforms, enterococci and Clostridium perfringens. The results indicate that there is no environmental threat due to the use of disinfected wastewater from both the inorganic and organic pollutants analyzed. In general, tertiary treatments improved the elimination/reduction of microbial contamination indicators, although both season and weather affected the efficiency of treatment. The parametric values for the inorganic and organic pollutants studied in drinking water are greater than those found in the disinfected waters studied. Disinfected wastewater allows us to save on fertilizers, mainly those with nutrients Ca, Mg and B. The use of disinfected wastewater in intensive horticulture by fertigation in the agricultural region of Almeria (southeast Spain) is considered.