The tailwater blind spot: Greenhouse gas hotspots in factory-style aquaculture cascades.

Factory-style aquaculture enhances production efficiency, yet its greenhouse gas (GHG) dynamics remain poorly constrained because tailwater units are often excluded from assessments of hydraulically connected multi-unit systems. Here, we investigated a factory-style freshwater aquaculture cascade, in which water flows sequentially through a source lake, an earthen pond, a semi-recirculating tank, an effluent settling pond, and a receiving canal. We quantified fluxes of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) during both farming and non-farming campaigns, identified influential environmental predictors using explainable machine learning, and explored model-based tailwater scenarios based on total ammonia nitrogen (TAN) reduction and dissolved oxygen (DO) enhancement. Water quality and GHG fluxes showed pronounced longitudinal gradients and strong unit-specific patterns. CO2 and CH4 were concentrated in downstream tailwater units, whereas N2O peaked in the earthen pond and remained elevated in the effluent and canal. Machine-learning attribution highlighted nutrient-related variables and the oxygen-pH gradient as important model-based associations with GHG flux variation across the cascade. Exploratory model-based scenarios for the effluent pond suggested that coordinated TAN reduction and DO enhancement may represent a testable direction for tailwater mitigation, although this response involved a trade-off with increased N2O. Excluding downstream tailwater units resulted in an approximately 79% underestimation of CO2-equivalent emissions, underscoring their importance in system-scale GHG accounting. These findings show that hydraulic connectivity within engineered aquaculture systems can redistribute GHG emissions along the production-tailwater continuum, revealing downstream tailwater units as critical components of whole-system emission assessments. Overall, this study provides a continuum-scale perspective for more comprehensive GHG accounting and for developing targeted mitigation strategies in hydraulically connected aquaculture systems.