I definitely agree that the reflectance results wouldn't be nearly as accurate as a lab sample, but for most purposes, the in-situ measurements with the fluorometer would be accurate enough for research. The time and effort required to obtain uniform chlorophyll samples in a marine environment with good primary productivity can be overwhelming. The last time I did it in the 2002 National Coastal Assessment (Corpus Christi, Texas and surrounding bay systems), I used a portable vacuum pump attached to a vacuum filtration apparatus that had to be sterilized after each use at each sampling site. Each resulting sample was collected on a filter paper, wrapped in aluminum foil, then stored in dry ice for transport to the lab. LOTS of work! If you have turbid water with really good populations in the plankton, these samples can require an inordinate amount of time to filter. Sand and detritus entrained in the water samples only increase the time required to process these filter samples.
I can certainly see the utility in actual water samples. Perhaps using OROV with the fluorometer AND a water sampling apparatus (discussed in other posts) would be a valid method of redundant sampling to help with final analyses.
Interestingly enough, our water sampling apparatus was almost identical to this one.
Ours was tied to the end of a nylon rope and the trigger weight was placed around the rope. We had depth markings on it so we would know what depth we were sampling from. Again, this sampling tube was required to be sterilized after each sample. This design works beautifully. I think I just came up with another idea for a peristaltic pump that could be mounted to OROV. You could figure your purge volume from the depth (length of sampling tube) and pretty much eliminate the need for sterilization between samples.