The use of ultrasound in resonators for manipulating particles in various biomedical applications is a relatively well studied topic. These studies were mostly concerned with steady‐state processes. However, in certain important applications, such as stirring and mixing fluids in microfluidics and biosensors, the time scale of a process plays a crucial role. In this presentation we consider some of these applications. In particular, the radiation force‐induced motion of microparticles and microbubbles in a swept‐frequency ultrasonic resonator is considered. The particles are forced to move due to switching the resonance modes in a resonator cell, thus providing effective stirring of the fluid. Another field of medical application of standing waves, where transient processes are of crucial importance, is ultrasonic treatment of tissues. In this new field of ultrasonic therapy, standing waves are used for producing lesions in the tissue with simultaneous monitoring the formation of the lesion by automatic controlling parameters of the standing wave field. The spatial and temporal distribution of ultrasound energy in the resonator containing treated tissue portion is theoretically analyzed. Dynamics of temperature changes in the tissue, which is important for optimizing tissue treatment regimes, is evaluated. Experimental data illustrating theoretical results are presented.