Abstract Growing anthropogenic activities are significantly influencing the environment and especially aquatic ecosystems. Therefore, there is an increasing demand to develop techniques for monitoring and assessing freshwater habitat changes so that interventions can prevent irrevocable damage. We explore an approach for screening the temperature-induced stress experienced by aquatic organisms owing to environmental variations. Luminescent spectra of upconversion [Y2O3: Yb, Er] particles embedded within Caridina multidentata shrimps are measured, while ambient temperature gradient is inducing stress conditions. The inverse linear dependence of the logarithmic ratio of the luminescence intensity provides an effective means for temperature evaluation inside aquatic species in vivo. The measured luminescence shows high photostability on the background of the complete absence of biotissues’ autofluorescence, as well as no obscuration of the luminescence signal from upconversion particles. Current approach of hybrid sensing has a great potential for monitoring variations in aquatic ecosystems driven by climate changes and pollution.