A major pathway in the biological carbon pump is the gravitational sinking of organic particles from the sunlit ocean (0–200 m) to the deep ocean. Variability in particle fluxes measured by sediment traps is often attributed to variability in primary production in the surface ocean. However, particle fluxes are also influenced by physical processes such as mesoscale eddies and fronts. In this study, we assess the impact of upper‐ocean dynamical structures on the variability of particle collection in the deep ocean. This is achieved by forward tracking the trajectories of 51.9 million virtual particles that were homogeneously released at a depth of 200 m with a constant sinking velocity of 50 m d− 1 in the Northeast Atlantic basin. Despite a homogeneous particle source without biological effects, we found that purely dynamical changes can induce heterogeneity in particle density and origin at depth. The position of sediment traps can thus significantly influence the weekly to seasonal particle collection in the deep ocean. Additionally, we identify and characterize nine particle clusters using a machine‐learning approach. The results show that the seasonality of particle collection at depth can be induced by seasonal variations in upper‐ocean flow structures. Clusters associated with eddy and frontal structures are found to intermittently contribute more than 50% of the particle amount during winter and spring, with smaller secondary peaks in the summer months. This study highlights the connection between mesoscale ocean dynamics and the spatio‐temporal pattern of conservative (non‐biological) particle collection in the deep ocean.