Environmental problems arising from aquaculture activities have been a concern worldwide, especially in Manila Bay. Thus, this study was implemented to identify the aquaculture practices of fish farmers and assess whether these practices are in accordance with the good aquaculture practices (GAqP) guidelines. Information was collected through survey and interview of fishpond operators from provinces around the bay. The study found that most fish farmers around the Bay do not observe the guidelines on GAqP evidenced by their high non-compliance with buffer zone, lack or utilization of improper water quality monitoring methods, non-implementation of important steps in pond preparation (e.g. soil testing), and application of illegal and noxious chemicals (e.g. cyanide). The calculated FCR, DMR and WPR in selected farms greatly varied. Farmers domesticated and/or allowed wading of animals on pond embankments predisposing contamination of both water and culture species. Anthropogenic activities such as sewage and garbage disposal, industry, and agriculture possibly added to deterioration of water quality in the fish ponds. On the other hand, notable practices were also observed in the areas such as the adoption of polyculture and semi-intensive fish farming methods, and the stocking of seeds from hatcheries.