The objectives of this study were to investigate the mutual effect of the PAHs fluorene and pyrene on their respective biodegradation and dissipation processes in an agricultural soil, and to determine the effect of hydroxypropyl-β-cyclodextrin (HPBCD), used to increase the bioavailability of PAHs, on such processes. Fluorene dissipation was primarily due to abiotic processes, although a small contribution from biodegradation was also observed. Therefore, fluorene dissipation did not increase with HPBCD and its presence did not significantly alter the dehydrogenase activity. In contrast to fluorene, pyrene dissipation depended primarily on biotic factors, with endogenous soil microorganisms capable of degrading pyrene, with large increases in dehydrogenase activity. HPBCD increased biodegradation rate of pyrene. The co-contamination of soil with both PAHs did not affect fluorene evolution, but significantly inhibited pyrene biodegradation. The different abilities of soil bacterial consortia to catabolize these PAHs are discussed. Additionally, the possibility that the abiotic loss of fluorene through volatilization had a significant effect on the microbial community biodegradation of both fluorene and pyrene is examined.