We investigate the influence of multiscale aggregation and deposition on the colloidal dynamics in a saturated porous medium. At the pore scale, the aggregation of colloids is modeled by the Smoluchowski equation. Essentially, the colloidal mass is distributed between different size clusters. We treat these clusters as different species involved in a diffusion-advection-reaction mechanism. This modeling procedure allows for different material properties to be varied between the different species, specifically the rates of diffusion, aggregation, deposition as well as the advection velocities. We apply the periodic homogenization procedure to give insight into the effective coefficients of the upscaled model equations. Benefiting from direct access to microstructural information, we capture by means of 2D numerical simulations the effect of aggregation on the deposition rates recovering this way both the blocking and ripening regimes reported in the literature.