This study evaluated effects of temperature and organic degradation on the persistence of δ13C and δ15N in aquaculture waste. Organic degradation time showed a significant linear (p<0.0001) and quadratic (p<0.0096) effect of depletion on δ13C and a significant linear effect (p<0.0001) of enrichment on δ15N. Temperature showed a significant linear effect (p<0.0001) of depletion on δ13C and a significant linear effect (p<0.0001) of enrichment on δ15N. Sediment samples collected from active sites showed δ13C values ranging from -22.55 to -20.94‰ and δ15N values ranging from 3.27 to 5.87‰. Inactive site sediment samples showed δ13C values ranging from -26.34 to -18.96‰ and δ15N values ranging from 4.02 to 12.12‰. Aquaculture feed δ13C values ranged from -21.07 to -17.32‰ and δ15N values ranged from 4.89 to 9.66‰. Organic degradation and temperature had significant effects on the persistence of δ13C and δ15N in aquaculture waste therefore reducing the potential for tracking aquaculture waste.