In biomedical and optical applications, multifunctional upconverting nanoparticles (UCNPs) play an essential role where non‐invasive temperature sensing and imaging are necessary. UCNPs smaller than 20 nm, which can be excited under 808 nm wavelength, are particularly promising in this area and can be implemented in humans or other mammals. However, new versatile nanoprobes are still needed for biology, especially for challenging studies of small aquatic invertebrates. Such tools allow better monitoring and understanding of their physiology, biochemistry, and ecological responses, which is crucial due to the growing pollution of water reservoirs and climate change. Herein, multifunctional NaYF4:Yb3+, Er3+@NaNdF4:Yb3+ core@shell NPs (15 nm), forming stable aqueous colloids, exhibiting intense emissions under excitation in the first biological window (808 nm), and presenting high thermal sensitivity and resolution related to the thermally coupled energy levels of Er3+ ions, are designed and synthesized. Such properties of UCNPs are further utilized for optical imaging of aquatic invertebrates (Daphnia magna) and temperature detection inside their bodies under 808 nm excitation. This pioneering application of NaYF4:Yb3+, Er3+@NaNdF4:Yb3+ demonstrates the high potential of developed UCNPs for multifunctional applications, especially for bioimaging and temperature sensing within whole organisms.