Aquaculture waters can be associated with the modification of the phytochemical profile in plants when they are used for irrigation; thus, Integrated Agri-Aquaculture Systems such as aquaponics represent a strategy to improve the bioactive content of medicinal plants. This study aimed to analyze the effect caused by cultivation using aquaponics on the modification of the content of bioactive compounds such as phenols, flavonoids, and apigenin in
Cuphea hyssopifolia and
Cuphea cyanea irrigated with
Cyprinus carpio waters. The results of each culture method showed unique differences (
p ≤ 0.05) in the concentrations of bioactive compounds and antioxidant activity in
Cuphea spp. For
C. hyssopifolia in aquaponics, 76% (61.08 ± 7.2 mg g
−1 GAEq) of phenols and 50% (5.62 ± 0.5 mg g
−1 CAEq) of flavonoids were maintained compared to 20% (16.99 ± 0.4 mg g
−1 GAEq) of phenols and 76.5% (8.19 ± 1.6 mg g
−1 CAEq) of flavonoids in conventional culture. For
C. cyanea in aquaponics, 91% (15.36 ± 0.8 mg g
−1 GAEq) of phenols and 47% (3.52 ± 0.6 mg g
−1 CAEq) of flavonoids were maintained compared to 24% (14.11 ± 1.3 mg g
−1 GAEq) of phenols and 82% (1.79 ± 0.1 mg g
−1 CAEq) of flavonoids in conventional culture. An increase of more than 60% in the apigenin content of
C. hyssopifolia in aquaponics confirms a eustress effect related to the use of
organically enriched waters. The results indicate that aquaponics can promote the biostimulation/elicitation of medicinal plants and increase their bioactive compounds, but this effect does not occur in the same way between species.
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