New techniques – called software sensors – issued from the non-linear automatic control field and initially developed for non-linear chemical systems have been applied to a continuous culture of phytoplankton. A software sensor (or observer) combines an analytical differential equation based model and partial measurements of the system in order to estimate the non-measured state variables. It filters data and estimates the actual state of living systems, models of which are often rough approximations. The efficiency of this approach is illustrated with a nitrate-limited chemostat experiment with the chlorophyceae Dunaliella tertiolecta performed in a computer controlled fluctuating environment.