Understanding the behaviour of soil and site in highly seismically active Assam valley, Shillong-Mikir Hills Plateau and Eastern Himalayan Syntaxis of Northeastern India is important for seismic hazard assessment. Constrained by this tectonic interaction, we estimate the ground motion parameters of these tectonic domains through the inversion of 129 three component strong motion records of earthquakes with magnitude Mw>4.0 & Mw<6.0. Remarkably, parameters estimated at 9 different sites help to classify the region into four different site class subjected to magnitude and epicentral distance of the earthquake. Higher spectral acceleration observed at low period in Diphu, Nongstoin, Tezpur and Guwahati infer embedded site condition as rock subjected to removal of source and path effect. On the other, low spectral acceleration at high period in Kokrajhar, Golaghat, Goalpara and Nagaon indicate distinctly thick alluvial basin. Fourier spectrum width in Guwahati, Diphu, Nongstoin and Tezpur, within 2-10 Hz indicate the presence of compact & hard subsurface strata while the broad spectrum width of Kokrajhar, Golaghat, Boko, Nagaon and Goalpara within 0.5 – 10 Hz suggests presence of loose alluvium soil or soft sediments. Simultaneously, site specific response study on 11/08/2009, M5.6 Myanmar-Manipur Border earthquake indicate that high spectral acceleration is evolved due to thrust mechanism. This integrative approach comprising site specific fourier spectra, design response, influence of fault type and horizontal to vertical spectral amplitude ratios offer an unique method to characterize the site in various seismically active regions of the world.