Summary: Communities of swimming microorganisms often thrive near liquid-air interfaces. We study how such ‘active carpets’ shape their aquatic environment by driving biogenic transport in the water column beneath them. The hydrodynamic stirring that active carpets generate leads to diffusive upward fluxes of nutrients from deeper water layers, and downward fluxes of oxygen and carbon. Combining analytical theory and simulations, we examine the biogenic transport by studying fundamental metrics, including the single and pair diffusivity, the first passage time for particle pair encounters and the rate of particle aggregation. Our findings reveal that the hydrodynamic fluctuations driven by active carpets have a region of influence that reaches orders of magnitude further in distance than the size of the organisms. These non-equilibrium fluctuations lead to a strongly enhanced diffusion of particles, which is anisotropic and space dependent. Fluctuations also facilitate encounters of particle pairs, which we quantify by analysing their velocity pair correlation functions as a function of distance between the particles. We found that the size of the particles plays a crucial role in their encounter rates, with larger particles situated near the active carpet being more favourable for aggregation. Overall, this research broadens our comprehension of aquatic systems out of equilibrium and how biologically driven fluctuations contribute to the transport of fundamental elements in biogeochemical cycles.