Reservoirs are an important nitrogen sink as a result of their retention effect, but their retention performance may vary with hydrologic conditions with time-varying characteristics, which also change them from being a sink to source over time. This study uses a coupled modelling system (Soil and Water Assessment Tool (SWAT) and a two-dimensional hydrodynamic and water quality model (CE-QUAL-W2) to analyze the nitrogen retention effect and influential factors at annual, monthly, and daily scales in Shanmei Reservoir in southeast China. The results showed that there was a positive retention effect of total nitrogen (TN), nitrate-nitrogen (NO3
-N) and ammonia nitrogen (NH4
-N) in most years, with average retention rates up to 12.7%, 7.83% and 26.17%, respectively. The reservoir serves mainly as a nitrogen sink at an annual scale. The monthly retention performances of TN and NO3
-N were observed during the wet season (April–October) with higher water temperature and lower velocity, while a release effect occurred during the dry season (November–March). For NH4
-N, which is prone to nitrification, the retention effect lasted longer, from May to December. The daily nitrogen retention process changed more dramatically, with the retention rate varying from −292.49 to 58.17%. During the period of dispatch, the regulated discharge was the primary factor of daily retention performance, while the hydraulic residence time, velocity and water level were all significantly correlated with nitrogen retention during the period without dispatch.
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