The ties that I'm most familiar with are with INRS in Quebec City, and NRCan and the Geological Survey of Canada. From a federal level, those are the groups—which are of course stationed in Quebec—that are the most influential in understanding and managing the St. Lawrence Seaway and, as you say, a huge drainage basin through Quebec and the surrounding areas into the St. Lawrence River.
I'm not clear on how that interacts with municipal and provincial governments.