A new, fully-automated, closed-chamber system was developed for measuring photosynthetic activity in aquatic plants, algae, or corals during immersion. The performance of this system, which monitors oxygen exchange, was evaluated both in the laboratory and in situ under natural conditions using the seaweed Laminaria digitata. Intact, large individuals were placed inside the chamber and kept in place by a plastic grid in a transparent Perspex dome. The grid separated the upper incubation chamber containing the alga from the detectors that were situated in the lower chamber. Oxygen was measured using a novel method based on lifetime optical fluorescence sensor technology that provides an extremely stable and precise measurement of dissolved oxygen. The circulation and homogenization of the medium between the samples and the detectors in this closed system were provided by two pumps. The medium could be renewed by another pump that opened to the external ambient seawater and controlled by a solenoid valve. All the mechanics were driven by an electronic card that allowed choice of filling time, time of measurement, and time of medium renewal. This system provides a new tool to study, in detail, the photosynthesis of whole aquatic organisms under natural field conditions during immersion, combining high time-resolution of oxygen exchange with a long temporal scale of in situ measurements. By allowing automatic and very accurate measurements without any intervention during monitoring, this system will be useful for estimating and comparing production of primary producers or for assessing the influence of environmental factors on production.