Site characterization of metropolitan areas, especially after an earthquake, is of paramount importance for interpretation of spatial damage distribution and taking measures that assure realistic design actions to strengthen existing constructions and create new ones. Such a case is the city of Durres, Albania, that was hit by the disastrous earthquake of 26 November 2019 (M6.4). Significant differences in structural damage were observed throughout the city, despite its uniform epicentral distance (approximately 15 km); this could be either due to varying vulnerability of the affected constructions and/or to spatial variation of strong ground motion in the city, resulting from local site effects; the latter factor was investigated in this study. This was achieved by taking single station ambient noise measurements throughout the city, at approximately 80 sites. Ambient noise measurements are favorable, as acquiring ambient noise data is an easy and effective noninvasive approach within urban environments. Measurements were processed using the widely applied Horizontal-to-Vertical Spectral Ratio (HVSR) method, following the SESAME project (2004) guidelines. Their fundamental and dominant frequencies, fo and fd, respectively, were calculated and related to the iso-depth contours of the investigated area, as well as their corresponding amplitudes, Ao, and Ad. These experimental parameters and the HVSR curves were used to group all examined sites into classes with similar properties. This clustering provided a zonation map with four categories consisting of similar shapes and amplitudes, applicable to the city of Durres. This map can be utilized as a first level zonation of local site effects for the city. In addition, dynamic properties of soil profiles in selected sites were investigated and tested using 1D synthetic ambient noise data, based on the Hisada (1994, 1995) simulation method, and compared to experimental HVSRs in proximity to the selected sites. A comparison of the proposed four categories zonation map to the observed damage of the 26 November 2019, mainshock is attempted and evaluated. The four categories zonation map with similar expected local site effects proposed in this study can be used as a first level seismic microzonation of Durres. Undoubtedly, corrections for 2D/3D effects on ground shaking must be applied to sites lying in the edges of the Durres basin.