This study implements an advanced high-throughput droplet microfluidics technique to cultivate uncultured CPR taxa from the groundwater of the Hainich Critical Zone Exploratory in Germany. The aim is to devised a cultivation workflow from groundwater microbial population harvesting, picolitre droplet encapsulation and incubation with soil extract and necromass supplements to imaging and genomic analysis of microbial communities. The established workflow is then used to enrich specific groundwater CPR taxa and characterize their diversity in comparison to classical bulk enrichments.