Large, sub-alpine, stratified lakes are directly within the scope of the European Water Framework Directive (WFD) and need adapted monitoring systems. Moreover, anthropogenic eutrophication was frequently the main cause of their water quality degradation in the 20th century. This paper is primarily aimed at demonstrating how in situ sensor-equipped buoys could be the base of monitoring designs to support the WFD objectives. The core of this paper, mainly methodological, focuses on single-depth, high frequency (4 per hour) fluorescence measurements. It shows that the internal wave pattern provides additional information to the single-depth time series to assess phytoplankton dynamics in a stratified water column displaying strong, vertical biomass heterogeneity. The paper deals with the following three aspects: (1) definition of an indicator to determine whether or not the sensor actually detects the metalimnetic fluorescence peak, (2) vertical representation of chlorophyll distribution from single-depth series; (3) time evolution of the fluorescence peak (maximum value, depth and associated temperature, peak width).