Bubbles have a strong optical signature and need to be removed from the water prior to making optical measurements. In addition to bubbles introduced by turbulence in the plumbing system, warming of the water and/or cavitation through the path can cause bubble formation. Further, during rough seas we experience significantly more bubbles in the system, likely due to exposure of the sea chest to hull turbulence.
A vortex de-bubbler (Ocean Instrument Laboratory, Stony Brook University, MSRC Vortex Debubbler, Model VDB-1), is the recommended hardware to remove bubbles. They typically come in two sizes: a 2 or 3 inch diameter model designed for a flow rate of 10 or 20 liters per minute, respectively. Using multiple debubblers in series does reduce the bubble impact in rough seas.