Measuring chlorophyll fluorescence at five different wavelengths provides the discrimination of four phytoplankton groups. Here the problems associated with a free-falling depth profiler for phytoplankton discrimination are considered. When F0, F, and Fm are determined sequentially in the same measuring cell, then the algae inside the cell have a different light history. It depends on their different locations in the cell as caused by the induction curve of chlorophyll fluorescence. Mathematical algorithms are developed which enable the calculation of the concentrations of individual phytoplankton groups from the integral fluorescence signal (averaged for 1s) for different velocities of the falling probe. The theory requires the knowledge of the fluorescence behaviour of phytoplankton in stationary suspensions. The predictions of the model are compared with measurements in flowing suspensions containing chlorophyta, cyanobacteria, cryptophyta and diatoms. The comparison shows the reliability of the algorithms. The application of the algorithms is indispensable for dark-adapted cells and is less important for light-adapted cells.