The Saguenay-St. Lawrence Marine Park (SSLMP) is a region that sustains a high abundance of zooplankton. The connectivity between zooplankton populations within the SSLMP and the surrounding areas was investigated for Calanus finmarchicus and C. hyperboreus. Deep-dwelling stage V copepodites (CVs) were collected in the Marine Park as well as in putative source regions in the St. Lawrence system in July 2009 (a time when they were entering into diapause). In May 2010, at the end of the overwintering period, diapausing CVs were sampled again in the Marine Park. To discriminate the origins and to predict the probable regions of origin of these deep-dwelling diapausing CVs in the SSLMP, a quadratic discriminant function analysis (QDFA) was performed. The classification algorithm was based on the carbon isotopic composition (δ13C) and percent carbon (%C) of individual copepods, as these variables are conservative when lipids are extracted prior to analysis. Our results suggest that about 23% of the Calanus spp. population sampled in SSLMP in late spring 2010 originated from the Saguenay Fjord (inside the SSLMP). The remainder of this population originated from regions outside the SSLMP, including the Lower St. Lawrence Estuary, and likely further east in the Gulf of St. Lawrence. Our results revealed high connectivity across the Saguenay and the St. Lawrence systems, as well as the potential for significant local production and recruitment of Calanus spp. within the Saguenay Fjord. This study also revealed the effectiveness of using δ13C as a marker in delineating the origin of Calanus spp., which has a relatively long non-feeding overwintering and diapausing period making it amenable to the conservation of isotopic signatures.