Mussels Mytilus galloprovincialis were cross-transplanted at South Portugal from a reference site (site 1) to a site more contaminated with hydrocarbon compounds (site 2), and vice versa, in an active biomonitoring (ABM) concept, to assess the biotransformation capacity catalyzed by the mixed function oxygenase (MFO) system. Total alkanes (TAlk), the unresolved complex mixture (UCM), and total polycyclic aromatic hydrocarbons (TPAHs) concentration increased respectively 6, 4.4 and 4.2 fold relatively to control, in mussels transplanted from site 1 to 2. In the cross-transplant, a 48, 57 and 62% depuration of TAlk, UCM and TPAHs concentrations occurred by the end of the 3–4th week. Petrogenic and biogenic (marine and terrigenous) sources of AHs, and petrogenic and pyrolitic (biomass and oil/fuel incomplete combustion) sources of PAHs were detected at both sites. CYP450, CYT b5 and NADPH-RED in mussels transplanted from site 1 to 2 were induced from day 0 to 28, with a total increase of 35, 32 and 35%, respectively, while biochemical equilibrium to lesser environmental contamination occurs in mussels transplanted from site 2 to 1. A significant relationship between CYP450 and NADPH-RED was found with TPAH, with distinctive behavior at the two sites. MFO system components increase with exposure time at one site and decreases in the other, reflecting an adaptation to distinct environmental hydrocarbon loads. The ABM strategy proved to be useful to understand the environment real impact on the biochemical responses in mussels’ local populations. In this study, CYP450 and NADPH-RED are a useful biomarker for hydrocarbon exposure.