Nowadays there is a growing interest to the natural evolutionary changes and especially those that driven by environmental pollution and climate change. Climate change in combination with human activities largely influences the environment and especially the aquatic ecosystems. We utilize photonics and nanoscale materials for non-invasive screening of stress felt by water organisms due to environmental variations. We present the results of real-time quantitative assessment of internal temperature and pH in aquatic species. The developed technique can be adopted and used for the studies of many other biosystems from terrestrial and aquatic invertebrates to fish.