This research analyzes for the first time in the Pacific Tropical-Subtropical Convergence off Mexico during June 2010 the relationships among the δ13C and δ15N signal distribution in the bulk zooplankton, water masses, and mesoscale structures. The environmental analysis showed that the California Current Water (CCW) and Transitional Water (TrW) converge where the 22 °C isotherm and 34.6 g kg−1 isohaline were observed (22°N). Two cyclonic eddies were detected: one in CCW at 24°N about 70 km in diameter, the other one located in TrW at 21°N with 150 km in diameter. A cluster analysis defined three zooplankton isoscapes with significant differences. Isoscape 1, immerses in CCW – the lowest δ13C (−22.37 ± 0.89 ‰) and δ15N (9.89 ± 1.32 ‰) – showed temperature (19.86 ± 1.97 °C), salinity (34.08 ± 0.37 g kg−1) values, the deepest thermocline (77.93 ± 25.51 m) and oxygen minimum zone (164.78 ± 44.96 m). The CCW was relatively oligotrophic without important mesoscale features in the sampled time within the sampled area. Isoscape 2, a cyclonic eddy in CCW – relatively enriched zooplankton δ13C values (−16.78 ± 1.95 ‰) due to the entry of enriched coastal biota– reflected in high chlorophyll a and subsequently assimilated into zooplankton tissues. Isoscape 3, a cyclonic eddy immerses in TrW – the highest δ15N (13.14 ± 1.60 ‰), salinity (34.76 ± 0.19 g kg−1) and temperature (19.90 ± 2.27 °C) values and shallowest thermocline (32.27 ± 18.63 m), and oxygen minimum zone (66.82 ± 37.68 m) in depth. Likely, this 15N-enriched recycled nitrate was pumped from the deoxygenated subsurface to the surface, reflected in the zooplankton bulks. The results showed that the isotopic signals in bulk zooplankton may be a good water mass and mesoscale activity tracer.