The Northwest Atlantic mackerel is comprised of northern and southern contingents that have distinct spawning grounds and migratory patterns centered off Canada and the US, but substantial mixing occurs between the two contingents in US fisheries, which likely varies over years and decades. Otolith carbon and oxygen stable isotopes (δ13C/δ18O) were analyzed to discriminate northern and southern contingents given that the two contingents are exposed to waters of different seawater δ18O and temperature in their juvenile period. Using archived otoliths and developing a classification baseline based on juvenile otolith carbon and oxygen stable isotopes, we assessed the degree of stock mixing in US waters during two phases of the US mackerel fishery (high landings: 1998–2000 year-classes; and low landings: 2011–2015 year-class). While strong discrimination occurred between the two contingents for 1998–2000 year-classes and the 2015 year-class baselines, the degree of discrimination was weak for the 2011–2014 year-class baselines. Random Forest classification for year-classes 1998–2000 showed that age-2 fish were mostly comprised of the southern contingent, whereas age 3+ fish were predominately the northern contingent, indicating strong incursion of the northern contingent into US waters. Classification of 2015 year-class fish indicated that age 2+ fish were dominated by the northern contingent, and the southern contingent were mostly absent from US waters. Results suggested that both contingents contributed to the US mackerel fishery during the period with higher landings, whereas during the most recent depleted phase, the US fishery was almost exclusively drawn from the northern contingent.