In order to evaluate the response mechanisms of L. gracilis fertigated with saline effluent from fish farming, L. gracilis plants were nourished with fish farming effluent with electrical conductivity of 0.45, 2.68, 4.60, 5.55 and 7.02 dS m− 1 for 60 days. The experiment was carried out in the open field using a completely randomized design with five treatments and four replicates. The salinity levels of the nutrient solution containing fish farming effluent did not affect the leaf and stem biomass production, relative water content and leaf area of the studied species. The activity of antioxidant enzymes varied when the nutrient solution salinity level was increased, which also stimulated the breakdown of starch reserves, but did not interfere with the biochemical parameters proline, photosynthetic pigments (chlorophyll a, chlorophyll b and carotenoids), levels of membrane damage and malondialdehyde, indicating that the plant showed no stress symptoms when fertigated with high-salinity effluent. The anatomy of L. gracilis leaf cross-sections shows a unistratified epidermis with glandular and non-glandular trichomes in the adaxial and abaxial sides. Plants that received only fish farming effluent (7.02 dS m− 1) showed a 25% reduction in the number of xylem bundles in the midrib region, compared to the control. The yield, chemical composition and antimicrobial activity of the essential oil extracted from L. gracilis leaves did not differ between treatments. Thus, the saline effluent from fish farming can be used in the fertigation of L. gracilis without compromising plant yield, avoiding environmental contamination with disposal in soil and/or water bodies.