In this study we measured the effects of using of secondary treated sewage effluent for irrigation (3.5 y) of a hardwood plantation (Eucalyptus or Casuarina) on the abundance and species composition of protozoa and nematodes in soil. Measurable populations of protozoa and free-living nematodes were observed in all treatments. Application of secondary treated sewage effluent had a stimulatory effect on the abundance of total and active protozoa and altered the species composition of all groups of protozoa and nematodes. In general populations were higher in soils under dripper lines than between dripper lines. Populations of protozoa were highest under Eucalyptus receiving sewage effluent and the difference between 'under dripper line' and 'between dripper line' was maximum in Casuarina plantation. A number of protozoan species belonging to genera Acanthamoeba (group 3 species such as A. castellanii) and Naegleria (i.e. potentially pathogenic protozoa) were observed in plots irrigated with secondary treated sewage effluent. Large (> 50 μm) amoebae and ciliate species were mainly observed in soils receiving sewage effluent. Bacterial feeding nematodes were the dominant group of free-living nematodes in all soils, and effluent irrigation increased their percentage especially in soil under dripper lines. Overall results in this study suggest that where heavy metal contamination is minimal, irrigation with secondary treated sewage effluent does not have significant negative effects on the abundance of protozoa and nematodes. Significant increases in the abundance of active protozoa and changes in species composition of protozoa and nematodes suggest an increased microbial turnover in effluent treated soils.