Municipal wastewater effluent is one of the largest sources of pollution to Canadian waters. Until recently, the disposal of wastewater was not of great concern to Arctic communities, but growing populations and urbanization bring more diverse contaminants that could cause deterioration of an already fragile environment. Bivalves have proven extremely useful in their ability to evaluate the importance and spatial distribution of contaminants. Thus, this thesis investigated the effects of Iqaluit’s (NU, Canada) primary treated municipal effluent in Frobisher Bay on the Arctic truncate soft-shell clam, Mya truncata. Clams were sampled from six locations along a gradient in proximity to Iqaluit’s wastewater effluent source. Four sites were chosen for their proximity and potential direct exposure to wastewater effluent and two were chosen for their distance and environmental barriers from the effluent source. Patterns of growth, stable isotopes and trace elements in the shell were linked to environmental variation on an annual scale and a parallel analysis measured the tissue-specific mRNA transcriptional response of the soft-shell clam. The results displayed slower growth and smaller shell lengths in organisms of the same age near the wastewater effluent source. Common side-effects of wastewater effluent like brackish water, increased organic input, and higher average calculated temperatures were evidenced by significantly lower ratios of carbon (1.38‰) and oxygen (1.31‰) isotopes in clam shells nearest the wastewater treatment plant (WWTP). Clams nearest the wastewater effluent source also had metals (lead and copper) characteristic of wastewater effluent accumulate in their shells over time. Given the environmental variation recorded in the shells near the WWTP, further evidence of chronic exposure impacts was supported by the cellular stress and xenobiotic response. The clams nearest the outfall exhibited lower expression of mRNA involved in the physiological response functions including antioxidants, metabolic regulators, molecular chaperones, and phase I and II detoxification response, but had heightened expression of mRNA of genes coding for enzymes that bind and remove xenobiotics. The culmination of these results demonstrates the presence of contamination and provides an early warning system into the possible adverse physiological changes that could result from chronic municipal wastewater exposure in Frobisher Bay.