How much does the weight of urban structures (buildings) affect the compaction (permeability, porosity, density) of alluvial sediments below a city?
This question might be more appropriate for the SE Engineering site.

The thing about soils is that they vary from place to place. Some are sandy, some contain more clay than others and the thicknesses of layers is also variable. All this influences how different soils react to surface loading stresses, such as from building foundations/footings.

Immediately below the footings the soils will experience the greatest stress increases. As discussed in this document, particularly from page 10 onwards, the magnitude of stress the soil experiences from footings decreases with depth - see the effect of a point load $Q$, applied to the surface, on the upper right of page 12. At a depth $z$, the vertical stress $\sigma_v$ has a certain higher value. At a depth of $2z$, the value of $\sigma_v$ is lower.

One reason why the affect of surface loads decreases with depth is due to the nature of soil particles and how they lie in relation to each other. Soil particles are not uniform in size or shape, so they rarely lie directly on top of each other. There are gaps between soil particles, called pores. The pores can hold ground water.

Compaction and consolidation of soils will reduce the volume (size) of pore spaces. Foundation loadings will only affect the soil beneath them.

Because soil particles do not lie directly on top of each other, one particle may lie above two or more particles, the stress exprienced by the upper soil particle will be transferred to the other particles. Providing the soil is deep enough, the affect of this is the to, over depth, transfer vertical stresses to horizontal stresses.

Ultimately, if a soil profile is deep enough, the stress the lower reaches of the soil experience due to urban development will be small and will not affect ground water movement.