Tracking techniques are vital for the understanding of the biology and ecology of organisms. While such techniques have provided important information on the movement and migration of large animals, such as mammals and birds, scientific advances in understanding the individual behaviour and interactions of small (mm-scale) organisms have been hampered by constraints, such as the sizes of existing tracking devices, in existing tracking methods. By combining biology, chemistry and physics we here present a method that allows three-dimensional (3D) tracking of individual mm-sized aquatic organisms. The method is based on in-vivo labelling of the organisms with fluorescent nanoparticles, so-called quantum dots, and tracking of the organisms in 3D via the quantum-dot fluorescence using a synchronized multiple camera system. It allows for the efficient and simultaneous study of the behaviour of one as well as multiple individuals in large volumes of observation, thus enabling the study of behavioural interactions at the community scale. The method is non-perturbing - we demonstrate that the labelling is not affecting the behavioural response of the organisms - and is applicable over a wide range of taxa, including cladocerans as well as insects, suggesting that our methodological concept opens up for new research fields on individual behaviour of small animals. Hence, this offers opportunities to focus on important biological, ecological and behavioural questions never before possible to address.