Tardigrades are microscopic animals widely known for their ability to survive in extreme conditions. They are the focus of current research in the fields of taxonomy, biogeography, genomics, proteomics, development, space biology, evolution and ecology. Tardigrades, such as Hypsibius exemplaris, are being advocated as a next-generation model organism for genomic and developmental studies. The raw culture of H. exemplaris usually contains tardigrades themselves, their eggs, faeces and algal food. Experimentation with tardigrades often requires the demanding and laborious separation of tardigrades from raw samples to prepare pure and contamination-free tardigrade samples. In this paper, we propose a two-step acoustomicrofluidic separation method to isolate tardigrades from raw samples. In the first step, a passive microfluidic filter composed of an array of traps is used to remove large algal clusters in the raw sample. In the second step, a surface acoustic wave-based active microfluidic separation device is used to deflect tardigrades continuously from their original streamlines inside the microchannel and thus isolate them selectively from algae and eggs. The experimental results demonstrated the efficient separation of tardigrades, with a recovery rate of 96% and an impurity of 4% algae on average in a continuous, contactless, automated, rapid and biocompatible manner.