The shallow structures of the Chalco and Xochimilco sub-basins (southeastern Mexico Basin) are established based on a seismic line that stretches trough both depressions. Interpretation of the seismic line was constraint by the stratigraphic column cut by the approximately 3000 m deep Tulyehualco well. The seismic line was converted to depth based on a vertical transverse isotropy velocity model determined from the interval, and root mean square (rms) velocities of the geologic units as established at the Tulyehualco deep well. P-wave modelling confirmed the results. The volcano-sedimentary infill established is consistent with the stratigraphic column of the 502 m deep MexiDrill borehole. It was possible to establish 1) the base of the fine stratified lacustrine sediments, and 2) the top of the basalts along the Xochimilco and Chalco sub-basins. The Xochimilco and Chalco sub-basins are separated by a shallow structural high (interpreted as due volcanic flows) against which the lacustrine sediments abut. A conspicuous anticline shaped structural high (adjacent to Xico tuff ring) divides the Chalco sub-basin into two depressions. The top of the basaltic basement matches with the upper volcanic unit horizon. In the western trough, the basement gets deeper from east to west (from 336 m at the structural high, to 660 m to the west). Immediately east of the anticline-shaped structural high, the basement is located at 510 m. Beneath the Xochimilco trough (at 180 m approximately) the volcanic basement shallows up smoothly northwestwards. In the eastern part of the Xochimilco sub-basin, the shallow lacustrian sediments are relatively thin. Northwestwards of the Tulyehualco well, their thickness diminishes. This apparent thinning is accounted by the fact that there the seismic line occupies the northern rim of the depression. Reflections in the upper 300 m of the section are not continuous. Beneath the central part of Chalco lake the reflectors are horizontal with a slight westward dip. At both sides of this central zone, reflectors are inclined or have dome shapes. This indicates that deposition along the Chalco sub-basin has been deformed. The thickness of the reflections associated with the fine laminated to volcanoclastic material transition zone is approximately constant, but thins and finally abuts against the structural high. In the eastern trough, seismic reflections at the shallow first 300 m are not as fine as in the western trough. These low magnitude seismic reflections might be associated with coarse fluvial volcanoclastic material from nearby Popocatéptl volcano. Seismic amplification in these two tectonic depressions by numerical modelling of seismic wave propagation can be based on the structure here established. Between 8 and 9 high amplitude reflectors in the first 300 m of the infill sequence are interpreted as due to impedance contrasts between geological units. Density and velocity logs along the MexiDrill borehole support this interpretation. Shallow strata are approximately 30 m thick. Towards the basin base, the strata are thicker (70 m approximately). These thicknesses are consistent with the nature of the volcano-sedimentary infill cut by the MexiDrill borehole. In particular, each seismic reflection would represent a sedimentation cycle of approximately 30,000 years (corresponding to a mean thickness of 30 m). If a sedimentation rate of 0.8 mm per year holds along the first 200–300 m of the basin infill (i.e., neglecting compaction effects, etc.) then this upper sequence comprises a record of paleo-ambiental changes that affected the southern Mexico Basin during the last 250,000 to 375,000 years.