Understanding the spatio-temporal dynamics of insects in agroecosystems is crucial when developing effective management strategies that emphasize the biological control of pests. Wild populations of Trichogramma Westwood egg parasitoids are utilized for the biological suppression of the potentially resistant pest species Helicoverpa armigera (Hubner) in Bt-transgenic cotton Gossypium hirsutum L. crops in the Ord River Irrigation Area (ORIA), Western Australia, Australia. Extensive, spatially-stratified sampling during a season of relatively high Trichogramma abundance found that spatial patterns of pest egg parasitism in the ORIA tend toward heterogeneity, and do not necessarily coincide with host spatio-temporal dynamics. Both patterns of host egg density and mean rates of parasitism are not good indicators of parasitoid spatio-temporal dynamics in ORIA cotton crops. Parasitism rates can be significantly higher within the middle strata of the cotton plant canopy before complete canopy closure, despite a similar number of host eggs being available elsewhere in the plant. Spatial variation in egg parasitism by Trichogramma in Bt-transgenic cotton is evident at the between-field, within-field and within-plant scale, and is not solely driven by host spatial dynamics. These factors should be considered when estimating Trichogramma impact on pest species during biological control and spatio-temporal studies of host-parasitoid interactions in general.