In this study we report 20 ancient shotgun genomes from present-day Western Hungary (3530 - 1620 cal BCE), mainly from previously understudied Baden, Somogyvar-Vinkovci, Kisapostag, and Encrusted Pottery archaeological cultures. Besides analysing archaeological, anthropological and genetic data, 14C and strontium isotope measurements complemented reconstructing the dynamics of the communities discovered at the site Balatonkeresztur. Our results indicate the appearance of an outstandingly high Mesolithic hunter-gatherer ancestry in the largest proportion (up to ~46%) among Kisapostag associated individuals, despite this component being thought to be highly diluted by the Early Bronze Age. We show that hunter-gatherer ancestry was likely derived from a previously unrecognised source in Eastern Europe that contributed mostly to prehistoric populations in Central Europe and the Baltic region. We revealed a patrilocal residence system and local female exogamy for this Kisapostag population that was also the genetic basis of the succeeding community of the Encrusted Pottery culture, represented by a mass grave that likely resulted from an epidemic. We also created a bioinformatic pipeline dedicated for archaeogenetic data processing. By developing and applying analytical methods for analysing genetic variants we found carriers of aneuploidy and inheritable genetic diseases. Furthermore, based on genetic and anthropological data, we present here the first female facial reconstruction from the Bronze Age Carpathian Basin.