A mechanistic state–space model has been developed to describe the dynamics of olive mill wastewater (OMW) treatment in phytoremediation pilot units with P. granatum L. and M. communis L. plants and to assess further the relative contribution of the plants in the overall OMW remediation process. Both phytoremediation and bioremediation processes have been considered in the model, i.e., phytodegradation, rhizodegradation, accumulation of hardly biodegradable organic matter on the root tissue of plants, microbial growth, maintenance and decay, and enzymatic decomposition of organics. Maximum specific microbial growth rates for bacteria and fungi were estimated within the range of 0.164–0.236 1/h. The specific rate for the decomposition of hardly biodegradable organics both by bacteria and fungi was within the range of 10.75–72.73 mg-substrate/g-biomass·h, whereas, particularly for the high-molecular-weight polyphenols, it was 1.02–18.25 mg-substrate/g-biomass·h. The values of the transpiration stream concentration factor were greater than 0.95 for both the non-phenolic and phenolic organics, which indicates almost passive uptake of OMW organics’ mixture by the plants. The corresponding factors for inorganic N and P were estimated as greater than unity, indicating active uptake. Overall, the model predicts the experimental data well when the organic concentration of OMW is high, and it predicts that phytoremediation processes contribute by more than 91% to the removal of OMW organics and nutrients, irrespective of the wastewater organic strength.