Animals can affect ecosystem processes through numerous pathways such as nutrient excretion, foraging, and bioturbation. Large grazing animals, including Florida manatees, may provide nutrient subsidies to aquatic biofilms via excreta when they migrate from the ocean to coastal springs in the winter for thermal refugia. Nutrient diffusing substrata (NDS) assess biofilm nutrient limitation using amendments of nitrogen (N), phosphorus (P), or both and comparing gross primary production (GPP) and chlorophyll a (chl a) in nutrient-amended and control treatments. We used NDS to study how migrating manatees from the ocean to spring-fed freshwater ecosystems affected biofilm nutrient limitation status in six coastal springs near Crystal River, Florida, before, during, and after the annual manatee migration. Manatees congregate in high numbers at three of the springs and do not congregate at the other three. Four patterns emerged: (1) biofilms were frequently co-limited by N and P when manatees were absent from the springs, but were never nutrient limited when manatees were present, (2) GPP and chl a in control treatments were lowest at all sites when manatees were present because manatee bioturbation buried NDS and likely induced light limitation, (3) manatee excreta had the potential to increase water column N by 6% and P by 13%, and (4) manatees affected the entire Kings Bay ecosystem by increasing total suspended solids from January through March (period of manatee migration) by 45% relative to the remainder of the year. These results demonstrate how migration of a large aquatic animal can affect ecosystem function through altering the physical environment and that manatee bioturbation effects override their nutrient inputs. Overall, these patterns suggest that manatees have the potential to increase nutrient export to the downstream estuary through excreta and decreased nutrient uptake, though these effects will be dependent on downstream conditions.