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Abstract Mesoscale eddies may enhance nutrient injection into the photic zone and ultimately the magnitude and composition of particle export to depth. Using satellite altimetry, we identified 38 cyclonic eddies that passed in close proximity to the Hawaii Ocean Time‐series (HOT) Station ALOHA, located in the North Pacific Subtropical Gyre, from 1993 to 2018. Particulate carbon (C), nitrogen (N), and biogenic silica (Si) export rates, measured using free floating sediment traps deployed at 150 m as part of HOT, were then associated with either the eddy core or edge based on distance to the eddy center and time of eddy evolution. Elemental fluxes varied significantly within and among individual eddies depending on season and eddy age. Spatially, biogenic Si fluxes were enhanced relative to particulate C and N fluxes at both the cores and edges, with temporally highest particulate C, N and biogenic Si fluxes occurring during the mature stage (3–8 weeks). On average, biogenic Si fluxes were 200 ± 80% (30–270% increase) higher relative to non‐eddy and during non‐bloom periods, with modest enhanced particulate C (10–30% increase) and N (10–20% increase) fluxes. In contrast, during the bloom season (July and August), elemental fluxes were all reduced by 20% relative to non‐eddy references, suggesting that cyclonic eddies depress export during the bloom period. Our results indicate that cyclonic eddies not only increase, but differentially impact the sinking export of critical biological elements, thereby contributing to long term ecological changes in foodwebs that rely on silica as well as carbon for growth.