The present study analyses transformation pathways of pristine and thermally treated porous limestone and dense marble surfaces by means of time-resolved streaming current and potential measurements coupled with scanning electron microscopy and in-situ X-ray diffraction. The results reveal that under nonequilibrium conditions the zeta potential (ζ) of natural carbonates may exhibit positive and negative signs and ζ drifts in opposite directions. Sample surface roughness influences ζ because it contributes to dissolution, as observed particularly in the initial period of time-resolved measurements. Thermal treatment causes a temporary charge reversal from negative to positive. The reactivity of calcium hydroxide on calcite surfaces governs the net electrokinetic potential and isoelectric point (IEPpH), even at low surface coverage, as cross-validated by in-situ XRD. It was also found that pore conductivity may lead to ~90% underestimation of ζ when assessed by streaming potential. SEM studies revealed micro cracks inducement on marble after thermal treatment, which can result in underestimation of ζ up to the same extent as for the porous limestone. ... mehrWhen an asymmetric cell configuration involving calcite and polypropylene surfaces is used, the fractional contribution of polypropylene to the IEPpH is 0.3 and to the overall determined ζ up to 0.5. Our findings contribute to the understanding of nonequilibrium and time-dependent electrokinetic potential modifications associated with the reactivity of porous surfaces. This study highlights the effectiveness of the streaming potential technique for monitoring such changes further supported by the use of ancillary techniques to analyze the extend of chemo-mineralogical and physical alterations.