Bead-based assays are incredibly popular in clinical and pharmacological settings for detecting single or multiple analytes. Separating and trapping beads are often integral steps, especially when such assays are conducted in microfluidic environments. Here, we report a first instance of the use of a capacitive micromachined ultrasonic transducer (CMUT) microarray for acoustically trapping silica beads within droplets into discrete, well-formed, circular clusters. We then demonstrate that the expansion and contraction of these clusters may be regulated via adjustments to the CMUT driving frequency. To our knowledge, this palpating action of aggregates has not been reported in other non-contact techniques. Bead manipulations are also replicated in a microchannel against flows with fluid velocities of 1.9 ± 0.2 mm s−1. The laminar flow conditions are exploited to sequentially trap bead clusters or separate large populations of beads into discrete streams by operating the CMUT microarray at threshold voltages. Unlike piezoelectric materials, CMUTs offer superior miniaturization through well established microfabrication techniques, better acoustic matching to fluids, and lower risk of sample heating. Thus, we believe this work illustrates the versatility of CMUT microarrays for use in future bead-based assays in lab-on-a-chip (LOC) platforms.