Nonphotochemical quenching (NPQ) is a well-known collection of different photoprotective mechanisms of plants and algae to avoid photodamage under an excess of light energy. In order to evaluate the overall effect of NPQ processes on the fluorometric determination of in vivo Chl a from a phytoplankton community dominated by diatoms, we compared the results obtained by two different fluorometric field devices with the total concentration of extracted Chl a measured by HPLC (in vitro Chl a). A different set of measurements were made to assess the performance of these fluorometers at high, moderate and low irradiance conditions. The Fbbe fluorometer, which is capable of distinguishing different algal groups according to their pigment content, allowed a better determination of in vivo Chl a under high irradiance conditions, with only a 10% mean difference from the in vitro Chl a concentration. In turn, the FMII fluorometer underestimated by as much as 50% the in vitro Chl a concentration under the same light conditions. As data from both fluorometers were in accordance with the in vitro Chl a values at moderate irradiance levels, the differences observed at high irradiances were attributed to the decrease in the yield of Chl a fluorescence caused by photoprotective NPQ processes. Accordingly, we estimated the effect of NPQ processes on the in vivo Chl a determination and the results allow us to provide an equation to correct this effect when in situ fluorometric measurements are carried out under high irradiance regimes. Our results demonstrate that under certain circumstances NPQ seriously compromises the results obtained by in situ fluorometric probes and highlight the need for a cautious interpretation of field data under such environmental conditions.