The Aquaponics Association has developed a set of provisional Good Agricultural Practices (GAPs) for aquaponics, a first step in enabling future food safety audits for large aquaponics operations. As these GAPs may run contrary to design of some current home gardens and artisinal farms, recall that GAPs are not mandatory for aquaponic systems that do not need to pass food safety audits.
FDA & USDA Resources for GAP Practices
Resources linked here for your convenience. These are general guidelines, while not specific to aquaponics provide a starting point for food safety.