The European Water Framework Directive and several other legislations worldwide have selected phytoplankton for monitoring the ecological status of surface waters. This assessment is a complicated task in coastal lagoons due to their intrinsic variability, prompting moves to use real-time measurements. Here, we tested the ability of the submersible spectrofluorometer FluoroProbe® to accurately estimate the phytoplankton biomass and to efficiently discriminate spectral groups in Mediterranean coastal lagoons, by using sub-surface water samples (n = 107) collected at Biguglia lagoon (Corsica) in different environmental situations (salinity and trophic state) from March 2012 to December 2014. We compared the estimates of biomass and phytoplankton group composition obtained with the FluoroProbe® (in situ and lab measurements) with the spectrofluorimetrically measured biomass and HPLC-derived quantifications of pigment concentrations. FluoroProbe® provided good estimates of the total phytoplankton biomass (particularly, the lab measurements). The FluoroProbe® data were significantly correlated with the HPLC results, except for the in situ measurements of very weak concentrations of blue-green and red algae. Our findings indicate that factory-calibrated FluoroProbe® is an efficient and easy-to-use real-time phytoplankton monitoring tool in coastal lagoons, especially as an early warning system for the detection of potentially harmful algal blooms. Practical instructions dedicated to non-specialist field operators are provided. A simple and efficient method for discarding in situ measurement outliers is also proposed.