In view of a water-energy-food (WEF) nexus strategy, the present work assessed the bioenergy production potential of Halimione portulacoides used for the phytoremediation of nutrient-rich simulated wastewater from saltwater-based integrated multi-trophic aquaculture (IMTA). Specimens of this halophyte plant were grown in hydroponics under four different nutrient treatments with distinct nitrogen (N) and phosphorous (P) concentrations. Ultimate and proximate analysis, calorific value and thermogravimetric analysis coupled to mass spectrometry were used to assess the bioenergy potential of the non-edible biomass of the plants, namely the canes (C) and roots (R), and of commercial pellets (CP), which were used as benchmark. R and, especially, CP had higher carbon but lower oxygen content and larger volatiles but lower ashes than C. The higher heating values (HHV) of C (16–17 MJ kg⁻¹) and R (17–18 MJ kg⁻¹) were the same order as those of conventional energy crops and CP (20 MJ kg⁻¹). Although mass loss and associated gaseous emissions during temperature programmed pyrolysis occurred mainly between 250 and 650 °C for all biomasses, they took place at slightly higher temperatures for C > CP > R. In any case, the integrated gaseous emissions during the pyrolysis of C, R, and CP were very similar and included H₂, CH₄, CO, and CO₂ (syngas main constituents). Biomass production of C was affected by the nutrients load of the applied treatments, but this was not the case for R. Also, the nutrients treatments had no detectable effects on the biomasses’ ultimate or proximate analysis, HHV, thermal decomposition or resultant gaseous emissions. Thermal properties and behaviour of C and R were very similar to those of CP, showing their potential for bioenergy production and revealing that a WEF nexus strategy can be implemented in IMTA by energetic valorization of non-edible biomass of H. portulacoides used for water phytoremediation.