The purpose of this study was to examine the health status and gametogenetic activity in Mya arenaria clams collected at various sites in the St. Lawrence Estuary (Quebec, Canada) and in the Odense Fjord (Denmark). Clam soft tissues were analyzed for metals/metalloids and organotin compounds to confirm their exposure to these contaminants. Their health status was assessed by a test battery of biomarkers designed to measure the early biological effects of contaminants, which include expression of defence mechanisms such as xenobiotic conjugation (glutathione S-transferase), expression of stress proteins (i.e., heme oxygenase and metallothioneins), changes in gametogenetic activity, and individual morphometric characteristics. Clam tissues were also examined for the presence of oxidative damage to lipids, formation of DNA strand breaks, and alterations in heme metabolism. The results showed that clams sampled from sites with either ferry activity or intensive boat traffic in marinas were contaminated by metals/metalloids such as Ag, Al, As, Co, Cr, Cu, Fe, Hg, Mn, Mo, Ni, Pb, Sn, V, and Zn. The clams also contained relatively high amounts of tributyltin (TBT) in their tissues (in the ng TBT/g range for both areas), with digestive glands containing more organotins than did gonadal tissues. Moreover, clams collected from TBT-contaminated sites had higher amounts of tin–heme adducts and lower total heme in their digestive glands. Condition factor, age distribution, and sex ratio were significantly altered in clams from impacted sites in the Saguenay Fjord and accompanied by an increased male/female sex ratio. Gametogenetic activity was also negatively affected, as revealed by reductions in gonadosomatic index, maturation index, aspartate transcarbamylase activity, and vitellogenin-like proteins. The Saguenay Fjord clams displayed a complex pattern of stress responses and damage such as increased heme oxygenase activity, phase 2 conjugation enzyme activity, lipid peroxidation, and altered DNA strand breaks. The integration of biomarker response data into a biomarker index at the whole-individual level (morphometric characteristics) and for various organs (gill, digestive gland, and gonad) revealed that, relative to the control site, morphological characteristics and gonadal activity were most affected at the most contaminated site, while the effects were more pronounced in the digestive gland and gill at moderately impacted sites. We conclude that the health status of M. arenaria clams at these contaminated sites is compromised, with obvious disruption of reproductive activity.