The Eastern Mediterranean contains two active tectonic borders: the Dead Sea Transform (DST) and the Cyprus Arc. Along the DST system of faults several deep sedimentary basins are found. Due to moderate seismicity and sparse spatial coverage of the Israel Seismic Network, ground motion analysis atop the basins is limited. In this paper, we present the results of two different approaches for ground motion amplification analysis. For the Amiaz Basin (Dead Sea region) we performed 3-D, high resolution numerical model using different source types and locations. We use the abundance of seismically induced clastic dikes to constrain the results of the numerical model and show the complexity of structure-source interaction. Specifically, we show the importance of seismic shielding by high velocity structures. For the Zevulun Valley, which underlays the densely populated and industrialized area of Haifa Bay, we present the results of seismic monitoring campaign using a transportable array. We calculate spectral amplification factors using out of basin reference stations and show the limitations of standard 1-D analysis.