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Self-organising maps (SOMs) were used to sort the excitation-emission matrices (EEMs) of dissolved organic matter (DOM) based on their multivariate 'fluorescence composition' (i.e. each parallel factor analysis (PARAFAC) component loading, viz. 'Fmax' value was expressed as a proportion of all Fmax values in each EEM). This sorting provided a simultaneous organisation of DOM according to differences in quality along a 125-km stretch of a large boreal river, corresponding with both source and season. The information provided by the SOM-based spatial organisation of samples was also used to assess the likelihood of PARAFAC model overfitting. Changes in fluorescence composition caused by changing salinity were also assessed for multiple sources. Seasonal and source-based differences were readily apparent for the main stem of the river and tributaries, and source-based differences were apparent in both fresh and saline groundwaters. Proportions of humic-like components were positively correlated with the amounts of bog, fen and swamp in tributary watersheds. Proportions of six PARAFAC components were negatively correlated with the proportions of all wetland types, and positively correlated with the proportions of open water and other land cover. Ancient saline groundwaters contained >50% protein-like DOM. There was no change in DOM quality from upstream to downstream in August or October. Increasing salinity was associated with additional protein-like fluorescence in all sources, but source-based differences were also apparent. The application of SOM to fluorescence composition is highly recommended for assessing and visualising transformations and differences in DOM quality, and relating them to associated properties.