Crete is actively seismic and site response studies are needed for estimating local site conditions subjected to seismic activity. In order to collect basic data, we performed ambient noise recordings to estimate the site response of the surface and near subsurface structure of the small-scale Kastelli Basin in northwest Crete. The spatial HVSR resonance pattern of the investigated sites in the centre of the Basin consists of either one or two peaks divided into low to high frequency range in different sites as follows: a) in some sites only one amplified peak at low frequencies (0.59 -1.23 Hz), b) in other sites only one amplified peak at medium frequencies (2.9 -8.54 Hz) and c) in yet other sites two amplified peaks in the low to high frequency range (0.59 -15.54 Hz). The investigated sites are amplified in the frequency range 0.59 -15.54 Hz while the amplitude reaches to a factor of 4 in the spectral ratios. The one HVSR amplified peak at low frequencies is related to locally soft or thick Quaternary deposits.Microtremors were measured in the coastal northwest part of the Basin in a well -lithified Cretaceous limestone site characterized by fractures and faults striking predominantly in a sector NNE to NNW. Sites of one amplified peak at medium frequencies are extended from coastal northwest to southwest delineating a structure striking to NNW. The two amplified peaks are attributed to shallow subsurface heterogeneities/irregularities, locally induced by fault zones and to the overlying Quaternary deposits.Spatial HVSR variations in the frequency and HVSR shape delineate four structures striking NNE, NNW and in a sector NW to WNW, crosscutting the dense populated Basin, suggesting that microtremors could be a valuable tool for providing a first approximation of fault zone delineation at least for the KastelliKissamos Basin. The Basin is classified into the X soil category of the Greek Seismic Code 2000.