Discharge from offshore activities to the sea may seriously affect the surrounding environment and cause disturbances in communities and ecosystems close to oil production installations. A major part of the waste released during oil production comes from produced water, including organic chemicals, metals and chemicals added in the separation and production process. The aim of this study was to investigate and quantify the effects of environmental relevant concentrations of produced water on fish in a long-term exposure. Gender-differences and changes over time were also investigated. Atlantic cod (Gadus morhua L.) were exposed to different concentrations of polycyclic aromatic hydrocarbons (PAHs) and alkylphenols (APs) for a total period of 44 weeks. The exposure consisted of three different treatments; “low” (2000 x diluted produced water), “high” (200 x diluted produced water) and “pulsed” (alternating control and high treatment on a weekly basis). The “control” treatment was made of water and acetone. Samples from the head kidney of cod taken before the start of the exposure and after 2, 16 and 33 weeks were analyzed using lysosomal membrane stability (LMS) and peroxisomal acyl-CoA oxidase (AOX) activity as biomarkers. Cod exposed to “high” and “pulsed” treatment had significantly lower lysosomal membrane stability than cod exposed to “control” treatment. No differences in lysosomal membrane stability between weeks of exposure or between male and female cod were found. Levels of peroxisomal AOX activity in the head kidney were significantly lower in cod sampled at 33 weeks of exposure compared to the activity found in cod sampled before start of the exposure. Significant differences in peroxisomal AOX activitiy were also found between male and female cod. There were no significant differences in cod head kidney AOX activity with regard to treatment groups. A correlation was observed between levels of PAH metabolites (1-OH-pyrene) measured in bile and lysosomal membrane stability in the head kidney of cod. The results from the present study clearly demonstrate that environmentally relevant concentrations of produced water components may have subtle effects on the health of fish in receiving waters. The results also revealed low and variable AOX activity in head kidney peroxisomes, indicating that the tissue may not be suitable for AOX activity measurements.