Due to the increasing concern of consumers about farmed fish contamination, in this study, different wild and farmed fish species (Nile tilapia (Oreochromis niloticus), gray mullet (Mugil cephalus), and thin lip gray mullet (Liza ramada) commonly consumed in Egypt, were chemically analyzed for the presence of heavy metals, antibiotics, polycyclic aromatic hydrocarbons, organochlorine pesticides residues, hormones and microbiologically evaluated for total counts of aerobic and coliform bacteria. Moreover, the influence of traditional cooking methods (i.e., grilling, frying, and baking) on these parameters were estimated. The results revealed that the polycyclic aromatic hydrocarbons and hormones were not detected in the fish species. However, heavy metals; cadmium, lead, nickel, cobalt, zinc, and mercury) were found in ranges of 0.014-0.35, 0.064-0.358, 0.027- 0.875, 0.058-0.750, 0160-1.345 and 0.062-0.426 mg/kg, respectively. In addition, the organochlorine pesticides residues (p,p1 -DDE, p,p1 -DDT, and Chlorpyrifos) in the studied fish samples ranged between 0.02-2.13 mg/kg in the marine sites only. The thermal treatments via grilling were the most effective cooking method followed by baking to decrease the heavy metals concentrations in the fish species. Also, all detected pesticide residues and antibiotics in different fish species were decreased by cooking methods. Generally, the studied cooking methods significantly (p<0.05) decreased the total bacterial count and coliform counts in all treated samples by %. The frying method was the most effective cooking method in decreasing bacterial counts. In addition, neither Escherichia coli nor Vibrio spp was detected in the fish samples. Moreover, the studied cooking methods seemed to be suitable for decreasing the studied contaminants. Consequently, the farmed and wild fish species in the studied sites in Ismailia Governorate, Egypt, were safe and suitable for human consumption. Periodical monitoring of all sites for pollutants is highly recommended to ensure consumer protection.