Previous research has focused on the removal characteristics of inorganic nitrogen in the integrated fixed-film activated sludge (IFAS) process. However, information on dissolved organic nitrogen (DON) is scarce, even though DON can be an important form of nitrogen in wastewater treatment plants with low-effluent total nitrogen. This study investigated the removal characteristics of DON in IFAS with three frequently used carrier filling ratios (FRs = 20%, 30%, and 40%). The results showed that effluent DON significantly decreased with an increase in the FR (p < 0.05, t-test). DON hydrophobicity-based fractionation combined with DON molecular composition analysis indicated that effluent DON from IFAS at FRs of 20% and 40% exhibits more lability than that at an FR of 30%, indicating that effluent DON at FRs of 20% and 40% is more prone to stimulate algae. This finding was also supported by an algal bioassay. As a result, there was no bioavailable DON (ABDON) removal increase when the FR of IFAS increased from 30% to 40% (p = 0.925, t-test). Gray relational analysis revealed that the metabolites dihydroceramide, 1-hexanol, and 3-sulfinoalanine had the greatest influence on DON bioavailability. Overall, this study indicates that operating an IFAS process with a higher FR cannot control the DON forms that readily stimulate algal growth.