Agricultural irrigation with wastewater effluent is a common practice in arid and semi-arid regions, and is used as a readily available and inexpensive option to freshwater. However, irrigation with effluents, which contain high levels of nitrogen, minerals, Dissolved Organic Carbon (DOC), detergents, microorganisms and toxic metals, may alter the microbial populations in soil, and thus affect soil fertility. We have studied microbial activities and biomass parameters in soils, affected by irrigation with wastewater. In addition, we followed the effect such irrigation has on community composition of Ammonia Oxidizing Bacteria (AOB) in soil. This group is responsible for the first, rate-limiting step in nitrification in which ammonia is transformed to nitrate via nitrite. We observed a change in several microbial activities in soils during irrigation with wastewater, changes that were dependent on the length of the irrigation period. The analyses were performed on several different soil types. The amoA fragment (coding for the ammonia monooxigenase) was PCR amplified and analyzed by DGGE (Denaturing Gradient Gel Electrophoresis) to monitor the AOB community. The different DNA fragments were sequenced and phylogenetically analyzed detecting an obvious difference in the phylogenetic groups of AOB developed following different treatments. While Nitrosospira-like bacteria dominated the soils irrigated with fertilized water, Nitrosomonas-like bacteria became dominant in effluent-irrigated soils.