Sustainable approach, cost-effective, precise and reliable outcomes become a great challenge in monitoring or re-evaluating the existing site-structure especially with minimum engineering database. Simple, fast, cheap, non-destructive, minimum handling operator and reliable findings of ambient vibration testing (AVT) and Horizontal to Vertical Spectral Ratio (HVSR) method has proven successful in site dynamic characteristics assessments of SK Sri Molek situated in Batu Pahat district, Johor, Malaysia. Although many expectations believed the survival of existing low-rise building is higher under earthquake threat, but moderate resonance effect was classified at similar study area from previous investigation. Determination of site fundamental frequency, Fo may assist further evaluation in seismic hazard assessments, ground condition monitoring as well as local soil characterization. The Fo were obtained from 2.05 to 4.07 Hz from the microzonation map produced with good verification presented between AVT outputs against two bore log records, for ground classification and sediment thickness predictions of sedimentary covers.