Abstract: An aquatic autosampler device for frequent collection of discrete samples of microorganisms at various locations and depths. The aquatic autosampler device moves a filter disk within a filter housing from a filter carousel into a filter housing holder. The filter housing holder, slidably mounted on a linear shuttle, moves the filter housing into a process position, where a syringe draws fluid in through a valve manifold and through the filter disk to collect samples on the filter disk. Reagents may then be passed over the filter disk to enable image-based identification and quantification of the cells on the filter disk. An imaging system on the autosampler may capture a fluorescent image of the microorganisms on the filter disk and store the image in a control computer. The filter housing may then be returned to the filter carousel for storage and further lab processing.