Dear @blair,
It looks your request is related to atmospheric correction over water surfaces. Sen2Cor processor is dedicated to atmospheric correction processing over land surfaces and is therefore not really adapted to retrieve accurate water properties.
If you are interested in performing more accurate atmospheric correction over water surfaces, we would recommend you to the following paper which compares different processors dedicated to atmospheric correction over water: ACIX-Aqua: A global assessment of atmospheric correction methods for Landsat-8 and Sentinel-2 over lakes, rivers, and coastal waters - ScienceDirect
If you want to test quickly on your images, as an example, the following processor may be one of the easier to set up and use: GitHub - acolite/acolite: ACOLITE: generic atmospheric correction module
We hope you find these suggestions useful.
Cheers,
@Sen2cor_dev_team