To increase the resilience of agroecological farming systems against weeds, pests, and pathogens, evolutionary breeding of diversified crop populations is highly promising. A fundamental challenge in population breeding is to combine effective selection and breeding progress while maintaining intraspecific diversity. A hydroponic system was tested for its suitability to non-destructively select root traits on a population level in order to achieve genetic gain and maintain diversity. Forty wheat progenies were selected for long seminal root length (SRL) and 40 for short SRL from a wheat composite cross population grown in a hydroponic system. Wheat progenies were multiplied, and a subset evaluated again in a hydroponic system. Preliminary tests in soil and competition experiments with a model weed were performed. The hydroponic selection for long SRL led to an increase of SRL by 1.6 cm (11.6%) in a single generation. Heritability for selection of SRL was 0.59. Selecting for short SRL had no effect. The preliminary soil-based test confirmed increased shoot length but not increased SRL. Preliminary competition experiments point to slightly improved competitive response of wheat progenies but no improved competitive effect on mustard. These results indicate a heritable selection effect for SRL on a population level, combining genetic gain and intraspecific diversity.