This study evaluated a polyhouse pond aquaculture system (PPAS, 200m2) for cultivating chocolate mahseer (Neolissochilus hexagonolepis) under Meghalaya’s agro-climatic conditions. Over two years, chocolate mahseer growth, survival, and biomass production in PPAS were compared against a conventional open pond aquaculture system (OPAS, 200m2). PPAS demonstrated substantial advantages, with fish exhibiting 34.6% higher final weight (112.24 ± 7.10g vs 83.38 ± 9.91g), 34.8% greater daily weight gain (0.31 ± 0.02 g/day vs 0.23 ± 0.03 g/day), 7.8% higher specific growth rate (1.10 ± 0.04 %/day vs 1.02 ± 0.08 %/day), and 16.1% better survival rate (83.85 ± 5.02% vs 72.20 ± 6.85%) compared to OPAS. Consequently, PPAS total fish biomass (941.97 ± 91.20 kg/ha) was 56.5% greater than OPAS (601.84 ± 90.60 kg/ha). PPAS maintained an average 2.4°C higher water temperature, with a 3.2°C difference during winter. Despite higher initial investment (₹ 85,000 vs ₹ 50,000) PPAS net profit (₹ 6,872) was substantially higher than OPAS (₹ 2,432) due to increased biomass. This innovative system mitigates environmental constraints, meriting further research for enhancing economic viability and long-term sustainability in adverse climatic regions.