The migration and clogging of fine particles in granular media are governed by complex interactions between interparticle forces and hydraulic loading. This study investigates the coupled effects of cohesion and hydraulic gradients on fines infiltration using a CFD-DEM framework. Macroscopic responses are characterised using indicators such as infiltration ratio, spatial distribution of infiltrated particles, and deposition coefficients, while microscale mechanisms are examined through dynamic evolution of interparticle contacts and contact force networks. The numerical results are validated against experimental observations for both cohesionless and cohesive conditions, demonstrating the reasonable capability of the model to capture fines migration and clogging behaviour. The results show that particle infiltration evolves through three distinct stages including initialisation, development and stabilisation. Cohesion promotes particle clustering and the development of stable contact networks that favour clogging, whereas hydraulic forces can destabilise these structures to enhance particle mobilisation. The balance between these competing mechanisms governs the transition between surface clogging, internal blockage, and continuous infiltration regimes. Microscale analyses further reveal that cohesion strengthens fine–fine contact networks and promotes stronger force transmission, while increasing hydraulic gradients progressively weaken these networks and enhance particle mobility. Overall, the novelty of this study lies in the mechanistic insight into the interactive role of cohesive and hydraulic forces in controlling fines migration and clogging processes in granular media.