In mass rearing of anopheline mosquitoes, pupae are usually separated from larvae on a daily basis to prevent unwanted adult emergence from trays. Depending on the device and species, 2 physical characteristics have most often been used for separation: buoyant density and size. In this report, we describe a system for continuous separation of Anopheles arabiensis larvae from pupae based on the natural difference in buoyant density and behavior between the 2 stages. We determined that temperatures 4–15°C caused neither mortality nor reduction in likelihood of pupation or emergence. Separation improved as temperatures decreased down to 4°C. We devised and demonstrated a 15°C water vortex separator that we anticipate can process approximately 1 million larvae and pupae per hour with a <0.3% pupal contamination rate and which operates unattended.