We study experimentally the creeping penetration of guest (percolating) grains through densely packed granular media in two dimensions. The evolution of the system of the guest grains during the penetration is studied by image analysis. To quantify the changes in the internal structure of the packing, we use Voronoï tessellation and a certain shape factor which is a clear indicator of the presence of different underlying substructures (domains). We first consider the impact of the effective gravitational acceleration on upward penetration of grains. It is found that the higher effective gravity increases the resistance to upward penetration and enhances structural organization in the system of the percolating grains. We also focus our attention on the dependence of the structural rearrangements of percolating grains on some parameters like polydispersity and the initial packing fraction of the host granular system. It is found that the anisotropy of penetration is larger in the monodisperse case than in the bidisperse one, for the same value of the packing fraction of the host medium. Compaction of initial host granular packing also increases anisotropy of penetration of guest grains. When a binary mixture of large and small guest grains is penetrated into the host granular medium, we observe size segregation patterns.