The treatment of high-salinity, low-carbon marine aquaculture wastewater poses significant challenges for biological denitrification. This study systematically evaluated the performance of a polycaprolactone (PCL)-based aerobic denitrification biofilter under varying temperatures (15 °C and 25 °C) and PCL addition levels (282, 564, 846, 1128, and 1410 g). Optimal nitrogen removal, total nitrogen (TN) removal efficiency exceeding 92%, was achieved with 1128 g PCL at 15 °C (HRT 10 h) and 1410 g PCL at 25 °C (HRT 8 h), significantly outperforming the low-PCL baseline treatment. Microbial community analysis revealed that increased PCL dosage promoted the dominance of the hydrolytic genus Flavobacterium over Simplicispira, enhancing polymer degradation capacity and system stability. Metagenomic sequencing further elucidated the complete PCL degradation pathway, wherein hydrolysis products were oxidized to generate NADH and FADH₂, serving as electron donors for denitrification. Key functional genes (narG, nirK, nosZ) and enzymes associated with both PCL decomposition and nitrate reduction were significantly enriched in high-performance reactors (e.g., AT15H6, AT25H6, ET15H10, ET25H10), correlating strongly with observed nitrogen removal rates. By integrating reactor performance with microbial ecology and functional genetics, this work provides a comprehensive “material–microorganism–gene–performance” framework, offering both practical strategies and mechanistic insights for enhancing denitrification in saline aquaculture systems.

The intensification of mariculture has increased nitrogen and phosphorus pollution in aquaculture wastewater. Conventional treatments often prove inefficient under saline conditions. To address this challenge, we developed an innovative aerobic denitrification reactor using Pseudomonas chloritidismutans K14, specifically tailored for seawater systems. Our study examined the effects of hydraulic retention time (HRT) and carbon-to-nitrogen (C/N) ratio on pollutant removal and critically assessed the physiological benefits for hybrid grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂). At an optimal HRT of 8 h and a C/N ratio of 8, the system achieved high removal efficiencies: 95.5% for NH₄⁺-N, 92.4% for NO₂⁻-N, 93.8% for NO₃⁻-N, 92.8% for total nitrogen (TN), and 84.8% for chemical oxygen demand (COD), along with a 47.3% reduction in total phosphorus (TP). More importantly, the system significantly enhanced grouper health by improving growth performance, digestive enzyme activities, and antioxidant capacity, along with a trend toward improved nonspecific immune indicators. The feed conversion ratio was optimized to 2.28, with a weight gain rate of 117.07%. Our findings establish this optimized aerobic denitrification system as an integrated strategy that effectively combines water purification with indirect health benefits, offering a sustainable solution for mariculture.