The dissolved organic nitrogen (DON) pool from algal-derived extracellular and intracellular organic matter (EOM and IOM) comprises proteins, peptides, free amino acids and carbohydrates, of which, proteins can contribute up to 100% of the DON. Previous reports of algal-derived DON character have focused on bulk properties including concentration, molecular weight and hydrophobicity. However, these can be similar between algal species and between the EOM and IOM even when the inherent molecular structures vary. A focus on bulk character presents challenges to the research on algal-derived nitrogenous-disinfection by-product (N-DBP) formation as N-DBP formation is sensitive to the changes in molecular structure. Hence, the main aim of this study was to characterize algal EOM and IOM-derived DON, specifically proteinaceous-DON, using a combination of bulk and molecular characterization techniques to enable a more detailed exploration of the relationship between the character of algal-derived proteins and the N-DBP formation potential. DON from the EOM and IOM of four commonly found algae and cyanobacteria in natural waters were evaluated, namely Chlorella vulgaris, Microcystis aeruginosa, Dolichospermum circinale, and Cylindrospermopsis raciborskii. It was observed that 77-96% of total DON in all EOM and IOM samples was of proteinaceous origin. In the proteins, DON concentrations were highest in the high molecular weight fraction of IOM-derived bulk proteins (0.13–0.75 mg N L−1) and low to medium molecular weight fraction of EOM-derived bulk proteins (0.15–0.63 mg N L−1) in all species. Similar observations were also made via sodium dodecyl sulphate polyacrylamide gel electrophoresis and liquid chromatography-high resolution mass spectrometry. Solid-state 15N nuclear magnetic resonance (NMR) spectroscopy of the EOM and IOM revealed the existence of common aliphatic and heterocyclic N-groups in all samples, including a dominant 2° amide peak. Species dependent variability was also observed in the spectra, particularly in the EOM; e.g. nitro signals were found only in the Cylindrospermopsis raciborskii EOM. Dichloroacetonitrile (DCAN) and N-nitrosamine concentrations from the EOM of the species evaluated in this study were lower than the guideline limits set by regulatory agencies. It is proposed that the dominant 2° amide in all samples decreased N-DBP formation upon chlorination. For chloramination, the presence of nitro groups and aliphatic and heterocyclic N-DBP precursors could cause variable N-nitrosamine formation. Compared to non-algal impacted waters, algae-laden waters are characterised by low organic carbon: organic nitrogen ratios of ∼7–14 and elevated DON and protein concentrations. Hence, relying only on bulk characterization increases the perceived risk of N-DBP formation from algae-laden waters.