Despite their complexity, ecotoxicological measurements using higher level responses remain a major tool in the assessment of ecosystem integrity. Nevertheless, the past decade saw an increasing number of cell based testing systems have found widespread application in ecotoxicology. One such test is bacterial bioreporters carrying a stress sensitive promoter fused to an easily detectable reporter gene. In the presence of a specific toxic stress,the expression cassette is switched on and the reporter gene is produced. This study evaluated the use of 14 different Escherichia coli bioreporter strains sensitive to different types of toxicity in the assessment of the ecological status of a small river basin in Flanders, Belgium. The river is fed at two geographically separate locations by two distinct and well-described effluents, one from a household sewage treatment facility and one from the discharge of the wastewater treatment facility of a large chemical plant. The results of the bacterial gene profiling assay were related to active biomonitoring results obtained through higher-level responses of caged Dreissena polymorpha, Chironomus riparius, and Cyprinus carpio deployed at the locations sampled for the bacterial assay. The results of the gene induction assay and the active biomonitoring data correlated well and corresponded to the flow dilution data, which is used here as a surrogate forthe chemical pollution gradient present in the river basin.