Natural populations are confronted with multiple selection pressures resulting in a mosaic of environmental stressors at landscape level. Identifying the genetic underpinning of adaptation to these complex selection environments and assigning causes of natural selection within multidimensional selection regimes in the wild is challenging. The water flea Daphnia is a renown ecological model system with its well-documented ecology, the possibility to analyze subfossil dormant egg banks, and the short generation time allowing an experimental evolution approach. Capitalizing on the strengths of this model system, we here link candidate genome regions to three selection pressures, known to induce micro-evolutionary responses in Daphnia magna: fish predation, parasitism, and land-use. Using a genome scan approach in space, time and experimental evolution trials, we provide solid evidence of selection at genome level under well-characterized environmental gradients in the wild and identify candidate genes linked to the three environmental stressors. Our study reveals differential selection at genome level in Daphnia populations and provides evidence for repeatable patterns of local adaptation in a geographic mosaic of environmental stressors fueled by standing genetic variation. Extensive, parallel genetic evolution at a genome-wide scale implies high evolutionary potential, relevant to understand the dynamics of trait changes in natural populations and their impact on community and ecosystem responses through eco-evolutionary feedbacks.