Estuarine ecosystems are characterized by a wide physical-chemical variation that in the context of global change scenarios may be exacerbated in the future. The fitness of resident organisms is expected to be influenced by such variation and, hence, its study is a priority. Some of that variation relates to water vertical stratification, which may create "environmental refuges" or distinct layers of water with conditions favoring the fitness of some individuals and species. This study explored the performance of juvenile mussels (M. chilensis) settled in two distinctive water depths (1 m and 4 m) of the Reloncavi fjord (southern Chile) by conducting a reciprocal transplants experiment. Salinity, saturation state and the contents of CO3 in seawater were among the factors that best explained the differences between the two layers. In such environmental conditions, the mussel traits that responded to such variation were growth and calcification rates, with significantly higher values at 4 m deep, whereas the opposite, increased metabolic stress, was higher in mussels raised and transplanted to the surface waters (1 m). Such differences support the notion of an environmental refuge, where species like mussels can find better growth conditions and achieve higher performance levels. These results are relevant considering the importance of M. chilensis as a shellfish resource for aquaculture and a habitat forming species. In addition, these results shed light on the variable responses exhibited by estuarine organisms to small-scale changes in the characteristics of the water column, which in turn will help to better understand the responses of the organisms to the projected scenarios of climate global change. (C) 2020 Elsevier B.V. All rights reserved.