Newly metamorphosed freshwater mussels are small and delicate, so that captive laboratory culture presents challenges for handling; for maintenance of suitable microhabitat, water quality, and food; and for avoidance of competitors and predators. To address these challenges, a new pulsed flow-through auto-feeding beaker system was developed for culturing juvenile mussels. In this system, groups of mussels were maintained in 300- to 1000-mL beakers with a thin layer of sand substrate. The water in the beakers was static except for pulses that were delivered every 1 or 2 h and that displaced about half of the water in each beaker per water cycle. A peristaltic pump delivered food to multiple mixing cells where the water was automatically mixed with food just before the water delivery. In testing this approach, newly metamorphosed mussels of 4 species were cultured in the system for 84 to 357 d. The sand and beakers were replaced weekly. Survival was high (>85% at day 84) for Lampsilis siliquoidea and Villosa iris, but relatively lower for Anodonta californiensis (29% at day 155) and Margaritifera falcata (23% at day 357). Growth rate ranged among the 4 species from 27 to 60 μm/d, with the slowest rate for M. falcata and fastest for A. californiensis. Overall, the new pulsed flow-through auto-feeding beaker system improved survival and growth of juvenile mussels versus other methods previously tested. Additionally, a simplified system for the water and food delivery was developed with a single mixing cell. The use of both systems indicate that they are suitable for laboratory experiments and for captive culture of juvenile mussels.