Aquatic mites (Hydrachnida, Oribatida, Halacaroidea) are diverse, and can reach high densities in the substrates of streams and rivers. Although they are a ubiquitous component of these habitats, their small size means that they are often overlooked. Using substrate samples from streams in tropical Queensland, I compared the thoroughness and time-based efficiency of three methods of extraction: sorting live samples without magnification (live-picking); exhaustive sorting of preserved samples using a dissecting microscope (microscope-picking); and kerosene-flotation of preserved samples followed by sorting with a dissecting microscope (kero-float). Live-picked samples yielded significantly fewer individuals and species than other methods, and were biased towards larger species. Oribatids and halacarids were not found when live-picking was used. Live-picking and kero-float methods provided similar numbers of mites per minute of sampling effort, whereas microscope-picking had a lower efficiency than kero-float. A combination of live-picking and kerosene-floatation is recommended for thorough surveys of stream acarofauna.