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Rapid changes in geotechnical and geological ground conditions lead to significant ground motion variability. This condition mainly occurs at the so-called basin edges, where there is an abrupt transition between soft highly compressible soils and stiffer materials. This problem becomes more relevant in areas where ground subsidence drastically changes the dynamic response of high plasticity clay deposits, such as those found in Mexico City, due to fundamental site period evolution with time. This paper presents site response analyses at an abrupt transition area in the southeast Mexico City region, along the edges of the Xochimilco-Chalco lakes. Considerable damage associated with three-dimensional wave propagation effects was observed in this zone during the September 2017 Puebla-Mexico earthquake. A series of three-dimensional finite difference numerical models of the basin edge were developed to evaluate ground motion variability, considering topographic effects and soil non-linearities. Good agreement between the computed response and the observed damage during the 2017 Puebla-Mexico earthquake reconnaissance was found. In addition, several normal and subduction events with a return period of 250 years were considered to evaluate the effect that frequency content, and strong ground motion duration have on the soil response variability. From the results gathered here, it was established the relevance of accounting for three-dimensional wave propagation fields to assess site effects at basin-edge zones properly and to be able to implement proper risk mitigation measurements at these zones. [ABSTRACT FROM AUTHOR]