Biofouling is an ongoing concern in aquatic environments and marine applications, leading to environmental impacts, contamination of aquaculture facilities, surface corrosion, decrease of hydrodynamic performance in ships and significant economic losses. Cyanobacteria are early marine surface colonizers and the most common fouling organisms on marine immersed surfaces. There is scarce information about marine biofilm reactors and their hydrodynamic characterization, which may enable them to mimic real environmental conditions. In this work, computational fluid dynamics was used to determine the shear rate field on coupons that were placed inside the wells of agitated 12-well microtiter plates. Biofilm formation by different filamentous cyanobacterial strains was assessed at two different shear rates (4 s-1 and 40 s-1) which can be found in natural ecosystems and using two different surfaces (glass and perspex). Biofilm formation was higher under low shear conditions and the hydrodynamic effect was more noticeable during biofilm maturation than during initial cell adhesion. This study highlights the use of 12-well microtiter plates as a high-throughput platform to mimic the hydrodynamics on aquatic environments and a promising approach to evaluate different surfaces or even compounds for biofouling control.