AbstractThe sinking of marine aggregates impacts the global carbon cycle as it is one of the primary sources of carbon export from the surface ocean. Aggregation and fragmentation alter the size of aggregates, which governs their sinking speed. Although aggregation theory is well established, aggregate fragmentation strength and breakup characteristics are less well understood. This study developed a cylindrical tank that formed and then exposed diatom aggregates to calibrated laminar shear through a combined rotating and oscillating motion. The shear rate was predictable using a developed analytical solution for the fluid motion within the tank. Under proper operating conditions, this facility provided fluid shear with a similar magnitude to that in multiple ocean environments. We also developed a unique image processing method that enabled continuous tracking of particles' position, size, and morphology as well as determination of the individual aggregate breakup events. The method has great potential to capture breakup events of large marine snow particles, quantify the aggregate morphological changes leading up to and at breakup, and provide data sufficient for statistical analysis of laboratory aggregate populations. We tested the method using laboratory‐cultured Odontella aurita and captured 79 breakup events of the resulting aggregates. These fragmented aggregates ranged from 1 to 5 mm in major axis length and underwent substantial morphological evolutions prior to the fragmentation.