In cooperation with Sitka National Historical Park, the South East Alaska Inventory and Monitoring Program (SEAN) has implemented several natural resource monitoring programs. The Indian River is the main freshwater feature of the park. The physical and chemical properties of the river, which are known as "water quality" and include measurements such as temperature and dissolved oxygen, have been monitored since 2010. Indian River streamflow has been monitored sporadically since 1988, and the network is currently exploring options for creating a stable, long-term program for collecting high-quality streamflow data. Both of these programs are vital to assessing the health of the river's ecosystem.
The park and SEAN also monitor pollutants from airborne, marine, and freshwater sources. Although Alaska is relatively pristine in comparison to other parts of North America, organisms living within the park are exposed to various pollutants from local sources, such as hydrocarbons from boats using internal combustion engines, and distant sources, such as mercury from coal-burning emissions depositing from the atmosphere.