A diesel contaminated groundwater site was surveyed using 16S rRNA gene based analyses to investigate the effect of bioaugmentation on the bacterial communities present. The analyses included the use of denaturing gradient gel electrophoresis (DGGE) to profile microbial community structure and the construction and sequencing of clone libraries in order to identify the organisms present. Community analyses revealed a high degree of similarity in the inoculated compartments during bioaugmentation, not observed once inoculation had ceased. However, it was also shown that there was very little community similarity between the inoculum and the inoculated samples. Instead, the similarity seen during the application of the bioaugmentation treatment was thought to be due to nutrient addition applied along with the inoculum. Furthermore, once the bioaugmentation treatment had ceased the communities around the site became more diverse, suggesting that the hierarchical structure seen during treatment was due to the stimulation of a group of opportunistic indigenous organisms by the nutrients added. The findings not only highlight the importance of monitoring the fate of inocula used in bioaugmentation but also how crucial the process of the selection of species and the culture conditions used in the construction of these consortia.