The expanding global demand for sustainable aquaculture underscores the need for efficient water quality management, particularly in controlling harmful nitrogenous compounds like nitrites. This study explores the effectiveness of Pantoea sp. A5, a nitrite-degrading bacterium isolated from food waste, reduces nitrite levels in aquaculture systems, focusing on the role of carbon sources like glucose and glycerol. The experiments showed that these carbon sources, especially glycerol, significantly enhanced the bacterium's ability to degrade nitrites across a range of temperatures without promoting growth, suggesting a cost-effective alternative to glucose. Unlike acetic acid, which did not enhance nitrite degradation, glycerol and glucose regulated metabolic pathways, evidenced by reduced malate dehydrogenase (MDH) activity and increased glutamate dehydrogenase (GDH) levels, facilitating efficient ammonia assimilation. These findings highlight the potential of using targeted carbon sources to manage nitrite levels in aquaculture, improving sustainability and contributing to global food supply efforts.