The aim of this research work is to identify the presence of pathogens, bacteria and protozoa, in different treated urban wastewaters and to relate biological pollution with the processes used in wastewater treatment plants. A study of the possibilities for water reuse is carried out taking into account bacterial and parasite composition. The analysed bacteria and protozoa are: Enterococcus faecalis, Pseudomonas aeruginosa, Staphylococcus aureus, Clostridium perfringens (spore), Salmonella spp., Legionella spp., helminths eggs, Giardia, Cryptosporidium spp. and free-living amoebae (FLA). The selected municipal wastewater treatment plants (MWTPs) are located in Navarra (Spain) and the main difference between them is the use of natural lagoons as tertiary treatment in some plants. The results concerning bacteriological identification showed contamination of mainly faecal origin, and the use of natural lagoons as tertiary treatment in some MWTPs produced an important disinfection effect. Moreover, pathogen parasites such as Giardia and Cryptosporidium were not detected in the samples studied although FLA were identified in all cases.