Green microalgae are able to produce molecular hydrogen in a clean way. H2 release is the result of complex, interacting, and transient intracellular mechanisms, influenced by extracellular conditions. To relate the dynamic coupling between culture conditions and biological responses, an original lab-scale photobioreactor has been developed. Such device allows to conduct cells culture under well-defined conditions, with on-line measurement of gas production. A first validation is conducted with a well-known protocol, the H2 production by Chlamydomonas reinhardtii under sulphur deprivation conditions. Instantaneous productivities were measured, and various successive physiological states were analysed and quantified. The proposed photobioreactor appears thus as an innovative tool for methodical optimisation of H2 production using photosynthetic microorganisms, including both bioprocess and physiological aspects in an integrated approach.