High molecular weight polymers are widely used in oilfield applications, such as in chemical enhanced oil recovery (cEOR) technique for hydrocarbon recovery. However, during flow in a porous rock, polymer retention is usually a major challenge, as it may result in the decrease of polymer concentration or lead to plugging of pores with significant permeability reduction and injectivity loss. Hence, an understanding of the retention mechanisms will have a profound effect in optimizing the process of polymer flooding, in particular, for carbonate rocks, which hold more than half of the world's oil reserves. Therefore, in this study, the retention of hydrolysed polyacrylamide (HPAM) polymer, a commonly used chemical for EOR, is investigated during flow in Estaillades carbonate rock. A novel approach of investigating HPAM retention in Estaillades carbonate rock was carried out using Atomic force microscopy (AFM). Since Estaillades carbonate rock is ∼98% calcite, HPAM retention was first characterised on a cleaved flat calcite mineral surface after immersing in HPAM solution. Afterwards, HPAM was flooded in Estaillades carbonate to observe the effect of flow dynamics on the retention mechanisms. We find that the dominant mechanism for retention of HPAM on calcite after fluid immersion is polymer adsorption, which we believe is driven by the electrostatic interaction between the calcite surface and the solution. The thickness of the adsorbed layer on calcite is beyond 3 nm suggesting it is not adsorbed only flat on the surface. Different types of adsorbed layers were formed representing trains, and the more extended loops or tails with the largest polymer layer thickness about 35 nm, representing the longer loops or tails. Layers of this thickness will begin to impair the permeability of the rock. However, in Estaillades, thicker adsorbed layers are observed in different regions of the rock surface ranging between 50 and 350 nm. We suggest that this is due to either mechanical entrapment and/or polymer entanglement during flow in Estaillades carbonate rock, which will cause the major permeability impairment in porous rocks.