Genetically engineered Pseudomonas putida reporters (BMB-PL and BMB-ME), which, respectively, carried phnS-luxCDABE and merR-egfp cassette, were used to determine bioavailable phenanthrene and mercury. Over a spiked range of concentrations and aged for 6 days in red soil samples, the reporters were tested to determine the optimal assay conditions and the bioavailable phenanthrene (0–60 mg kg−1) and Hg2+ (0–240 μg kg−1) were evaluated by the signal of the relative fluorescent units and relative luminescence units. Single contamination was carried out and good correlations were obtained between signal strength and pollutant concentrations, whereas interference and bioavailability repression were observed in dual-contamination experiments. Other heavy metal ions at nanomolar level did not interfere with BMB-ME measurement while BMB-PL showed some response to other polycyclic aromatic hydrocarbons or their intermediate products during degradation. Comparing high-performance liquid chromatography methods with the bacterial reporters, both BMB-ME and BMB-PL appeared to have a detection limit (mercury <40 μg kg−1; phenanthrene <24 mg kg −1) similar to the instrumental analysis. Although physical parameters may affect the interaction of pollutants with bioreporter cells, advantages include the inherent biological relevance of the response, rapid response time, and potential for field deployment. Our results strongly suggest that the BMB-ME and BMB-PL bioreporters constitute an adaptable system for easily detecting the bioavailability of mercury and phenanthrene in the red soils.