Atlantic salmon were fed extruded diets based on either 100% fish oil (FO) or 100% vegetable oil blend (VO) substitution for 22 months. A total of seven distinct feeding periods were studied that incorporated higher levels of dietary oil inclusion, and larger pellet size as fish size increased. Whole fish levels of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/F) and dioxin-like PCBs (DLPCB) were analysed at the beginning and end of each of the seven feeding periods. The PCDD/F and DLPCB concentrations in the FO diets increased from 2.43 to 4.74 ng WHO-TEQ kg−1 (TEQ, toxic equivalents), while VO diets decreased from 1.07 to 0.33 WHO-TEQ kg−1 as oil inclusion increased. Partial least square regression analyses identified feed concentration, growth rate and feed utilization, but not variations in lipid content, as factors significantly affecting fish PCDD/F and DLPCB levels. Accumulation efficiencies for DLPCB (740 ± 90 g kg−1) were significantly (P < 0.01) higher than for PCDD/F (430 ± 60 g kg−1), explaining the increasing dominance of DLPCB levels over PCDD/F levels in whole fish (DLPCB : PCDD/F ratio of 2.4 ± 0.1 for both VO and FO fed fish) compared with feed (DLPCB : PCDD/F ratio of 1.5 and 0.34 for FO and VO feed respectively). Vegetable oil substitution significantly reduced the level of PCDD/F and DLPCB (eightfold and twelve-fold, respectively) in the fillet of a 2 kg salmon, but, also negatively affected beneficial health components such as fillet n-3/n-6 fatty acid ratio.