This study aims to investigate Donax trunculus (D. trunculus) as a biomarker for heavy metals and total hydrocarbon contamination. To achieve this goal, we investigated the effect of 3 day-depuration on the accumulation levels of heavy metals and total hydrocarbons as well as the transcriptional variations in expressions of oxidative stress-related genes of Donax trunculus collected from El-Gameel region, Port Said, Egypt. After 3 day-depuration, all the accumulated tested heavy metals levels showed a considerable decrease (levels after depuration divide by levels before depuration) in D. trunculus tissues by 23%, 20%,72%,98%, 89%, 66% for Pb, Cd, Cu, Fe, Mn and Zn respectively. Additionally, the concentrations of total hydrocarbons in clam's D. trunculus tissues were reduced to 95%. After 3 days of treatment, the results revealed that the Cat activity decreased to approximately 36% and expression of CYP gene had been up-regulated by about 38%, The Gst gene had been down-regulated by about 2-fold in D. trunculus. Additionally, Mt gene had been up-regulated to approximately 70% and SOD gene had been down-regulated to 50%. To conclude, accumulated heavy metals and total hydrocarbons measured before depuration in the soft parts of D. trunculus was higher than the standard worldwide acceptable limits leading to the hypothesis that D. trunculus in the investigated study area may not be safe for human consumption. Therefore, as a potential public health threat from the seafood diet, more research on the chronic toxic effects of heavy metals and total hydrocarbons in marine species are needed.