Colloid deposition in granular media is relevant to numerous environmental problems. Classic filtration models assume a homogeneous pore space and largely ignore colloid aggregation. However, substantial evidence exists on the ubiquity of aggregation within porous media, suggesting that deposition is enhanced by it. This work studies the deposition process in relation to aggregate size and structure. We demonstrate that aggregation is induced at typical groundwater velocities by comparing the repulsive DLVO force between particle pairs to the hydrodynamic shear force opposing it. Column experiments imaged with high-resolution X-ray Computed Tomography were used to measure aggregate structure and describe their morphology probability distribution and spatial distribution. Aggregate volume and surface area were found to be power-law distributed, while Feret diameter was exponentially distributed with some flow rate dependencies caused by erosion and restructuring by the fluid shear. Furthermore, size and shape of aggregates are heterogeneous in depth, where a small number of large aggregates control the concentration vs depth profile shape. The range of aggregate fractal dimensions found (2.2-2.42) implies a high potential for restructuring and/or breaking during transport. Shear-induced aggregation is not currently considered in macroscopic models for particle filtration, yet is critical to consider in the processes that control deposition.