The aim of this study was to determine the effect of pesticides on free-living soil nematodes in a desert system. Spatial and temporal distributions as well as changes in nematode community structure were investigated. Soil samples were collected monthly between November 2000 and November 2001 from four plots: one treated with Nemacur, one with Edigan, one with water and one untreated plot as control. The nematode population as well as spatial distribution was found to be affected by treatments on a temporal basis. The different treatments applied led to a significant difference in the abundance of nematode trophic groups, where the fungivores and bacterivores were found to decrease in the pesticide-treated samples. A total of 31 genera were found in the samples, with 21 in the Nemacur-treated sample and 16 in the Edigan-treated sample. Ecological indices such as trophic diversity, maturity index and Shannon index elucidated the effect of pesticides on density, diversity and trophic group composition.