In contaminated aquatic ecosystems, it is expected that organisms suffer some effects caused by the contaminants. However, for mobile organisms inhabiting heterogeneously contaminated ecosystems, the continuous exposure to contaminants can be avoided by moving to less contaminated habitats. The present study evaluated the habitat selection of the freshwater shrimp Atyaephyra desmarestii experimentally exposed to different copper concentrations to verify whether the heterogeneous contamination distribution and the connectivity between habitats with different copper levels could generate a random population distribution similar to metapopulation. The experiments were performed in the HeMHAS (Heterogeneous Multi-Habitat Assay System), a non-forced multi-compartmented exposure system, in which it is possible to simulate the distribution of contaminants in a linear gradient or as patches of contamination. Copper was used to simulate a linear contamination gradient (26 to 105 μg/L Cu) and two patchy scenarios with three contamination levels [reference zone (R: 26 ± 7 μg/L Cu), mixing zone (M: 61 ± 2 μg/L Cu) and disturbed zone (D: 101 ± 12 μg/L Cu)], with two mixing zones or one central mixing zone in a heterogeneous scenario. In the copper gradient scenario, a clear trend of shrimps (59.6 ± 8.0% of the population) moving to the reference zones and an avoidance of 66.7 ± 11.1% of the most contaminated zone were observed. For the patchy scenarios, a random distribution of organisms (34, 36 and 30% for R, M and D zones, respectively) was observed in the scenario with one mixing zone; on the other hand, a slight preference for the reference zones (44.9 ± 4.8%) was evidenced in the scenario with two mixing zones. As shrimps are able to select less contaminated areas, it is highly important to preserve clean zones in heterogeneously contaminated environments, such as the arrangement in meta-ecosystems, as the less- or uncontaminated zones might represent less stressful areas to protect populations against continuous contamination exposure.