Measurements of chlorophyll fluorescence will be dependent upon the short term light-acclimation state of the phytoplankton (termed non-photochemical quenching), which in turn is affected by the residence time of the water within the plumbing system (or within an illuminating instrument). This effect result in an underestimation of chlorophyll, if otherwise the instrument is well calibrated and will be observed as a decrease in fluorescence with increased ambient light (and lab light if pipes are transparent).
In addition, fluorescence by CDOM, if significant in the water, contaminates the measurements by chlorophyll fluorometers (e.g. Proctor and Roesler, 2010). A recent review by Roesler et al., (L&O Method submitted) covers all the known issues associated with this measurements.