This study endeavours to assess the seasonal stability of the microtremor horizontal-to-vertical spectral ratio (MHVSR) method using a portable weak motion seismometer at four selected sites in the Srinagar city of Kashmir Valley. The aim was to understand the effect of seasonal changes in the groundwater table on the site response. In this regard, two sites having coarse-grained deposits and two with fine-grained deposits were chosen for testing through the months of September 2023 to May 2024. Seasonal variations were captured through testing in a dry spell followed by a brief rainfall spell in the summer, a wet spell due to snowfall in winter, and a long spell of rain in the springtime. The results show that the HVSR amplitude at high frequency exhibits a 30–40% seasonal variation with a maximum in winter and a minimum in summer, although the frequency value essentially remains the same. The deviations in amplitude indicate the change in the stiffness of the shallow soil layer due to the fluctuation of the moisture content, the changes being more evident in fine-grained soil sites. Random noise due to high water content after precipitation was also seen to exaggerate the amplitude peak at low frequencies, leading to unreliable results. It is evident that the shallow depths are susceptible to changes in environmental and anthropogenic activities, and therefore, the corresponding HVSR amplitudes must be used with great caution for the resonance assessment of structures as well as to constrain the shear wave velocity in the joint fit modelling technique.