Freshwater ecosystems are increasingly subjected to mounting pressures as a result of intensive agricultural activities, rapid urbanization, and the growing demand for food production. Within this context, aquaponics and biofloc technology have emerged as promising and environmentally responsible alternatives for aquaculture, offering integrated systems that recycle nutrients, minimize water usage, and enhance both fish productivity and plant growth. This study evaluated the growth performance of Clarias gariepinus fingerlings reared in three systems: biofloc, aquaponics with jute (Corchorus olitorius), and a combined biofloc–aquaponic–jute system. Fingerlings (average length: 10.5 ± 0.50 cm; weight: 6.55 ± 0.30 g) were stocked in outdoor 500‑L tanks at a density of 200 fish/m³. Biofloc was initiated using jaggery, while aquaponic units consisted of gravel substrates (1 m²) planted with 50 jute seedlings/m², connected to fish tanks via aquarium pumps (Haizhi®). After 60 days, fish survival did not differ significantly among treatments (P > 0.05). However, absolute growth (75.50 ± 2.30 g) and specific growth rate (1.31 ± 0.12 g) were significantly higher in the biofloc–aquaponic treatment (P < 0.05). The length–weight relationship exponent (b) was 2.09, 2.95, and 3.06 for biofloc, aquaponic, and biofloc–aquaponic systems, respectively. Jute shoot dry biomass was also greater in the biofloc–aquaponic system compared to aquaponics alone. These findings demonstrate that integrating biofloc with aquaponics not only enhances nutrient availability for plants but also optimizes fish growth and health, offering a sustainable approach to freshwater resource management.