Dissolved organic matter (DOM) plays a significant role in the nutrient supply, energy flow, and pollutant transportation in the wetland ecosystem. However, little is known about the effect of the decomposition of different organic materials in alpine wetland water on the DOM characteristics. By conducting a 90-day decomposition experiment with the addition of different organic materials (peat soil, yak manure, and plant litter) alone or their combinations into alpine wetland water, we characterized the water DOM using three-dimension excitation-emission matrix spectroscopy. The results showed that the decomposition of organic materials significantly affected the chemical properties, sources, humification degree, and composition of the water DOM. The decomposition increased dissolved organic carbon and dissolved total nitrogen in the water. For most of the water samples, a fluorescence index ranging from 1.4 to 1.7 and a biological index of less than 0.8 may indicate that both autochthonous and allochthonous sources contributed to the water DOM, which may primarily rely on allochthonous sources. UVA (37.55–46.81% of total fluorescent components) and UVC fulvic-like substances (29.91–35.53% of total fluorescent components) dominated the water DOM compositions. Among the treatments, additions of peat soil and yak manure led to the highest and the lowest humification degree of the water DOM, respectively. For the treatment of the combination decomposition of all three organic materials, the yak manure may stimulate microbial activity and facilitate the decomposition of plant litter and peat soil and, therefore, boost the humic-like substances in the water DOM. These findings may help the development of wetland biomass management with the objective of maintaining alpine wetland ecosystem services.