The Southeast Pacific coast is renowned as the world’s most productive regions, primarily due to upwelling of nutrient-rich subsurface water. While numerous studies have emphasized the importance of surface eddies, subsurface eddies such as Peru-Chile Undercurrent (PCUC) eddy, Puddies, remain largely underexplored. This study utilizes a high-resolution two-level nesting simulation coupled with a biogeochemical model to elucidate roles of eddies at two distinct layers, the surface (upper 50 m) and subsurface layer (σθ=25.5-26.5 kgm−3). A Lagrangian particle tracking was used to understand the fate of nitrate transported by subsurface eddies. Our results reveal that cyclones dominate the surface layer, while anticyclonic Puddies, prevail in the subsurface. The roles of subsurface eddy-driven nitrate flux vary in space. In the southern Peruvian region (16.5◦S-18.5◦S and 71◦ W-81◦ W), we show that more predominant onshore subsurface eddy fluxes directed northeast as opposed to the offshore flux caused by surface eddies. Meridionally averaged onshore nitrate flux in the offshore region is driven almost entirely by subsurface eddy-induced flux in the middle of the characteristic PCUC density, σθ = 26-26.25 kgm−3. Subsurface eddy flux of nitrate averaged within subsurface layers accounts for ≅10-20% of total onshore and offshore transport in latitude range 16.5◦S-18.5◦S and from 18.5◦S to the south, respectively. Furthermore, the Lagrangian particle tracking shows that Puddies originated in the southernmost area travelled to the northwestern regions, resupply nitrate onshoreward that is otherwise flown away poleward by the PCUC. This Puddy- induced nitrate resupply contributes 15.4% to the nitrate that reaches coastal upwelling zone.