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An assessment of the severity and extent of aquaculture impact and the estimation of sustainable carrying capacity were undertaken in three areas of the Philippines - Bolinao (marine site), Dagupan, (brackishwater) and Taal Lake (freshwater). This paper describes the potential mitigating measures that could be taken to reduce nutrient release from aquaculture, increase nutrient uptake using extractive species, and possible early warning systems for critical states of the tide when there is reduced flushing.