Anything but water located along the beams is a blockage and affects the data.
When a transmitted sound pulse hits something and gets reflected, the registered Doppler frequency shift represents the velocity of that object and not the water. It is hence not valid velocity data of water. This means that any data influenced by blockages should be discarded. If the blockage only concerns one beam and the data from the other beams are reasonable, it can be considered to exclude one beam in the post-processing of the data.
Sound waves don't just stop when they encounter an obstacle. Instead, they propagate beyond this and we can get valid velocity measurements further out in the profile. However, this depends on the size and characteristics of the blockage. More precisely, it depends on how much of the signal's energy gets absorbed or reflected by the obstruction, and how much energy is "left" in the pulse that propagates further. Ultimately it depends on the quality of the data behind the blockage, and because of that, it is essential to assess correlation and Signal-to-noise ratio in these areas.
Many things can block the beams, such as rocks, ropes, buoys, trawl balls, animals, underwater structures, sediments, etc. Figure 1 shows an illustration of possible blockages. Once the left beam encounters the stone wall, the rest of the profile is blocked. But, since the chain from the buoy is situated in a much smaller area of the right beam, it may be possible to get valid measurements beyond this blockage. The red cells are the ones that should be discarded directly due to blockages. If an obstacle partially extends into a cell, the entire cell still needs to be discarded because we cannot distinguish where in the cell it is.
Figure 1: Illustration of possible beam blockages.
Figure 2 provides an example of how a blockage can be seen in amplitude data. The amplitude readings in space and time present a blockage almost 20 meters from the instrument in the first half of the measurement period. The same blockage is found in the amplitude profiles by spikes because most blockages reflect stronger than the scattering particles in the water.
Figure 2: Overall amplitude of a data set showing a blockage in the first half (top), and the same blockage showed in the amplitude profiles as spikes (bottom).
Blockages can also be due to tidal burial of the transducers and fouling. Tidal burial is most relevant for bottom-mounted instruments that regularly get covered by masses from the seabed due to tidal waves dragging the masses. The result is periodic changes in data quality that follow the approximately two high and two low tides throughout the day. Figure 3 shows how this can be seen in the amplitude. In this data set, the signal strength is low when the sea level rises. This is when the transducers are buried. The signal strength further out in the profile is severely reduced compared to the signal strength when the transducers are not covered.
Figure 3: Tidual burial of transducers when the sea level rises.
As the amount of blocking material increases with growth, fouling can become problematic when measuring over a long period. The consequence may appear as a gradual decrease in amplitude with time, as presented in Figure 4. Velocity measurements beyond the fouling may be valid for quite a long time until the fouling becomes massive and absorbs or reflects too much of the transmitted signal. One way to reduce fouling is to attach antifouling patches on the transducers.
Figure 4: Gradual decrease in amplitude due to fouling.