In Jeju Island, multiple land-based aquafarms were fully operational along most coastal region. However, the effect of effluent on distribution and behaviours of dissolved organic matter (DOM) in the coastal water are still unknown. To decipher characteristics of organic pollution, we compared physicochemical parameters with spectral optical properties near the coastal aquafarms in Jeju Island. Absorption spectra were measured to calculate the absorption coefficient, spectral slope coefficient, and specific UV absorbance. Fluorescent DOM was analysed using fluorescence spectroscopy coupled with parallel factor analysis. Dissolved organic carbon (DOC) and total dissolved nitrogen (TDN) were measured using high-temperature catalytic oxidation. The DOC concentration near the discharge outlet was twice higher than that in natural groundwater, and the TDN concentration exponentially increased close to the outlet. These distribution patterns indicate that aquafarms are a significant source of DOM. Herein, principal component analysis was applied to categorise the DOM origins. There were two distinct groups, namely, aquaculture activity for TDN with humic-like and high molecular weights DOM (PC1: 48.1%) and natural biological activity in the coastal water for DOC enrichment and protein-like DOM (PC2: 18.8%). We conclude that the aquafarms significantly discharge organic nitrogen pollutants and provoke in situ production of organic carbon. Furthermore, these findings indicate the potential of optical techniques for the efficient monitoring of anthropogenic organic pollutants from aquafarms worldwide.