Environmental variability drives adaptive responses, yet how organisms with minimal genetic diversity adapt remains unclear. Using invasive Daphnia pulex (JPN1 lineage), we demonstrate that phenotypic integration—coordinated trait expression—mediates environmental adaptation despite limited genetic divergence. We found that environment-dependent integration drives stress adaptation more strongly than genetic distance, with differential plasticity dynamically reorganizing trait correlations. Notably, digestive enzymes (particularly lipase) and body size showed tightly coordinated responses to resource limitation, revealing how phenotypic networks reorganize under stress. By developing a quantitative framework to track these genotype-environment interactions, we show how integration facilitates adaptation in genetically impoverished populations. These results challenge the paradigm that genetic divergence is essential for phenotypic adaptation and provide mechanistic insights into invasion success. Our approach bridges invasion biology and eco-evolutionary theory, offering predictive tools for understanding rapid adaptation in diverse asexual systems facing environmental change.