A method for automatically counting and measuring sizes and motility behavior of zooplankton and phytoplankton in water samples is presented. Two video cameras are focused on separate optical chambers of different sizes. The chambers are filled and emptied repeatedly by synchronized pumps. Real-time motion analysis is performed by computer on the respective video feeds. Fluorescence from chlorophyll a (Chl a) is imaged at single pixel resolution. Measured parameters for individual organisms include size, swimming velocity, motility patterns, and chlorophyll fluorescence density. The system was tested during a mesocosm experiment where it was mounted on one of several mesocosm columns. The results were validated against Chl a measurements and microscopy counts. A sampling interval of 1 per day revealed detailed dynamics of chlorophyll activity as well as shifts in both the phytoplankton and zooplankton community structure over the course of a month. A helix coefficient, a metric related to organism motility behavior, showed substantial variation over time, consistent with changing plankton communities. Sampling rates as frequent as 1 per hour enables detailed analysis of diurnal vertical migration and similar phenomena at fixed sampling points.