There is a variety of vegetation along the Alagnak such as spruce, willows and many types of berry bushes (salmon berries, blackberries, blueberries, and cranberries). Fiddlehead ferns, wild celery, and sourdock are also present and collected by subsistence users.
During the summer of 2002, the NPS Inventory and Monitoring division conducted a vascular plant inventory. Their goal was to document 90% of all vascular plants occurring within the Alagnak River corridor and Katmai National Park and Preserve (adjacent to the Alagnak). During the summer field surveys, a total of 523 specimens were collected, recorded, and pressed. Approximately 130 species are new records for the area. A number of discoveries present significant range expansions of species. For example, a population of Dupontia fisheri, a tundra grass of northern and northwestern Alaska and northern Siberia, was found at Swikshak Lagoon over 200 miles east of its previously known range. Additionally, it is the first time it has been recorded in a woodland marsh in Alaska. Carex filifolia, a sedge, was found on a mountainous ridge above Swikshak Lagoon, approximately 450 miles to the southwest of its known range.