In piled raft systems (PRSs), the piles are used to support load or to control settlements. These systems, when founded in soft soils that are then consolidated by loads or subsidence processes, can induce negative friction in the piles and other phenomena related to variations in the distribution of load or settlements. This paper presents the results of physical modeling in a geotechnical centrifuge capable of different distributions of piles under a raft. As a result, the influence of consolidation and extraction of water from a deep soil layer on the behavior of the PRS model was analyzed. It was determined that the processes associated with the extraction of water from the deep soil layer induce larger settlements. A separation between the raft and the soil is possible, as well as a change in the behavior of the PRS.