Palm Oil Mill Effluent (POME) treatment ponds play a dual role in pollutant removal and greenhouse gas (GHG) emissions. This study examines the relationship between water quality parameters and methane (CH₄) fluxes across a tropical multi-pond POME treatment system operating under continuous loading. Field monitoring was conducted along a sequential anaerobic–facultative–aerobic pond train, measuring CH₄ fluxes and key physicochemical parameters, including chemical oxygen demand (COD), total suspended solids (TSS), and ammonia nitrogen (NH₃–N). Results revealed a pronounced spatial gradient, with CH₄ flux decreasing from 4,931.3 mg m⁻² h⁻¹ in the early anaerobic pond to 2,758.5 mg m⁻² h⁻¹ in the final polishing pond, indicating a transition from methanogenic to more oxidative conditions. Multivariate regression analysis identified ammonia (R² = 0.68, p < 0.01) and TSS (R² = 0.54, p < 0.05) as strong positive predictors of CH₄ emissions, whereas COD exhibited a significant negative association (R² = –0.47, p < 0.05). These results suggest that methane emissions are more closely linked to substrate bioavailability and nitrogen-mediated microbial processes than to total organic load alone. Elevated ammonia concentrations likely reflect active ammonification and enhanced buffering conditions that favor methanogenesis, while non-biodegradable COD fractions and acidification may constrain CH₄ production. This study provides new insight by highlighting ammonia as a key predictor of methane emissions and by demonstrating a non-linear relationship between organic load and GHG release in tropical POME pond systems. Integrating pollutant removal efficiency with emission mitigation strategies—such as controlled aeration, biofilm enhancement, and nitrogen management—is therefore essential for sustainable POME treatment.