This study was carried out to compare between the hygienic quality of fish and water used in different aquaculture types. A total of  56 water samples and 150 fish samples also were collected from different aquacultures in Egypt. Water samples were tested for the presence of three heavy metals as Cadmium (Cd), Lead (pb) and copper (cu). Also, it were examined for theirPhysicochemical characteristics. Both water and fish samples were examined bacteriologically Total bacterial count(TBC), Total coliform count (TCC) and Feacal coliform count(FCC). Also, Results revealed a significant increase in NH₃ of pond samples, TBC , FCC, Cd, pb and Cu of  both water and fish samples in fresh aquacultures compared to marine aquaculture. While a significant increase in No₃, Ca²⁺,  Mg²⁺, T.ALK , TDS, EC and Cl^-  in water samples of marine aquaculture in comparsion with fresh aquacultures.
This difference between  two types of fish farms may attributed to natural chemistry of water used in each farm, which in turn influence the hygienic quality of the fish produced from each farm , where marine water affect the heavy metal accumulation on fish negatively either by competitive inhibiton through ions exchange in gills or by forming un absorbable precipitate. Also, the high salinity of marine water sets up a hypertonic environment which enhance bacterial death. Also, many types of bacteria are killed by the high concentration of NaCl in marine aquaculture.