I have been looking at more lidar data in CARIS today with one of my committee members and am now starting to really figure out how CARIS displays the data. In my previous post I mentioned that the peak with the green line represents the determined depth and the peak with the red line represents an "alternate depth." This "alternate depth" designation in CARIS is somewhat misleading, as this peak actually represents the small amount of energy from the green (532 nm) pulse that is reflected by the water surface. The reason that the peak appears larger, in some instances, than the bottom return is presumably due to the gain settings being amped up so a detection could be made.
Looking at the image below, this does seem to make sense. In this dataset, 3 peaks can clearly be seen. In CARIS, the 1064 nm and 532 nm returns are shown on the same graph, with the first x number of bins coming from the IR return, and the remaining bins coming from the green return. The first unmarked peak represents the IR return from the water surface. The red marked peak is the 532 nm surface return ("alternate depth") and the green marked peak is the 532 nm bottom return. If you look under the lidar tab, the depth for the "alternate depth" is 0.16 m, which becomes negative (out of the water) once a tide value is applied. I am assuming that this depth reading is due to the fact that the green surface return, though nominal, would still have a slight penetration through the water surface. It could also be related to the difference between the IR detected distance to the water surface and the green detected distance to the water surface.