Lake Bosten is the largest inland throughput freshwater lake in the northwest arid zone of China. In recent years, the lake ecosystem and the drinking water safety of the surrounding residents have been seriously affected by the increase in human activities and wastewater discharge in the basin, and the impact of riverine input on the lake water quality needs to be focused on. In this study, the three-dimensional fluorescence spectra of coloured dissolved organic matter (CDOM) measured in summer and autumn were analysed in parallel.Three fractions of CDOM from Lake Bosten were identified: terrestrial humic fraction C1, tyrosine-like fraction C2 and tryptophan-like fraction C3. The effect of river input on the DOM of Lake Bosten was also analysed based on Pearson correlation. The results show that river input’s influence on Lake Bosten’s DOM differs between seasons and is directly related to the seasonal changes in river water quality. In summer, the water entering the lake from the Kaidu River mainly comes from winter snowmelt and carries a large amount of terrestrial humus into the lake, while in autumn, it is mainly glacial meltwater. The content of terrestrial humus is reduced as the flow into the lake increases, showing that the overall DOM concentration near the estuary is higher in summer and lower in autumn. The three components C1, C2 and C3, were found to be more abundant in the western part of the lake where the Kaidu River and the Yellow Water Ditch enter the lake, and the three components were similarly affected by seasonality. The correlation between DOM and conductivity was also carried out at sampling points near the mouth of the Kaidu River and other areas. It was found that the influence of external river input on the DOM of Lake Bosten was mainly concentrated near the mouth of the river, and the relationship between DOC and CDOM in the area near the mouth of the river was significant so that the CDOM could be inferred by remote sensing before estimating the DOM content. The study of the influence of river inputs on the composition of dissolved organic matter in Lake Bosten in different seasons is of great importance to protect the lake’s ecological environment and improve the lake’s water quality.