Polydimethylsiloxane (PDMS) is a soft, biocompatible polymer extensively employed in biomedical research, notable for its tunable mechanical properties achieved through cross-linking. While many studies have assessed the mechanical properties of PDMS utilizing macroscopic and microscopic methods, these analyses are often limited to freshly prepared samples. However, the mechanical properties of PDMS can be expected to change during prolonged exposure to water or air, such as interface polymer chain loosening or surface hardening, which are critical considerations in applications like cell culture platforms or microfluidic devices. This paper presents a comprehensive 10-day investigation of the evolution of PDMS surface mechanical properties through AFM-based nano-indentation. We focused on the most commonly utilized crosslinker-to-base ratios of PDMS, 1:10 (r10) and 1:20 (r20), under conditions of air and deionized water storage. For r10 samples, a hardening process was detected, peaking at 2.12 ± 0.35 MPa within five days for those stored in air and 1.71 ± 0.16 MPa by the third day for those immersed in water. During indentation, the samples displayed multiple contact points, suggesting the formation of distinct regions with varying mechanical properties. In contrast, r20 samples exhibited better stability, with an observed elastic modulus averaging 0.62 ± 0.06 MPa for air-stored and 0.74 ± 0.06 MPa for water-stored samples. Relaxation experiments, interpreted via the General Maxwell Model featuring two distinct component responses, a relatively consistent fast response τ1 (on the order of 10−1 s), and a more variable, slower response τ2 (on the order of 10 s), throughout the study period. The identification of two distinct relaxation times suggests the involvement of two disparate material property regimes in the relaxation process, implying changes in the surface material composition at the interface with air/water. These variations in mechanical properties could significantly influence the long-term functionality of PDMS in various biomedical applications.