This study investigated the transformation, bioavailability, and seasonal changes of dissolved organic nitrogen (DON) in nitrogen removing biofilters (NRBs) treating domestic onsite wastewater. The results demonstrated that NRBs were able to remove 92.6–94.3% DON from septic tank effluent with low effluent DON concentrations (0–5.8 mg N L–1), comparable to the levels detected in the tertiary municipal wastewater treatment plant. Both hydrophilic and hydrophobic DON were efficiently removed by the sand filters, while additional hydrophilic DON (0.8–1.8 mg N L–1) was produced in the lignocellulose/sand layer due to soluble microbial product formation. Seasonal change (i.e., temperature variation) did not impact the effluent DON composition or its removal efficiency by NRBs, while higher concentrations of hydrophilic DON (1.7–2.5 mg N L–1) were detected in the final effluent during the summer months (16.4–22.9 °C). DON in the NRB effluent had a higher potential to stimulate algal growth than other nitrogen forms (NH4+ and NOx–), confirmed by higher chlorophyll-a concentrations observed in the bioassay tests. The results suggest the DON levels in the final effluent of an onsite wastewater treatment system shall also be considered in onsite wastewater quality management and the effluent discharge regulations.