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The extensive use of a geographic information system (GIS) and remote sensing in ecological risk assessment from a spatiotemporal perspective complements ecological environment management. Chromophoric dissolved organic matter (CDOM), which is a complex mixture of organic matter that can be estimated via remote sensing, carries and produces carcinogenic disinfection by-products and organic pollutants in various aquatic environments. This paper reports the first ecological risk assessment, which was conducted in 2016, of CDOM in the Yinma River watershed including riverine waters, reservoir waters, and urban waters. Referring to the risk formation theory of natural disaster, the entropy evaluation method and DPSIR (driving force-pressure-state-impact-response) framework were coupled to establish a hazard and vulnerability index with multisource data, i.e., meteorological, remote sensing, experimental, and socioeconomic data, of this watershed. This ecological vulnerability assessment indicator system contains 23 indicators with respect to ecological sensitivity, ecological pressure, and self-resilience. The characteristics of CDOM absorption parameters from different waters showed higher aromatic content and molecular weights in May because of increased terrestrial inputs. The assessment results indicated that the overall ecosystem risk in the study area was focused in the extremely, heavily, and moderately vulnerable regions. The ecological risk assessment results objectively reflect the regional ecological environment and demonstrate the potential of ecological risk assessment of pollutants over traditional chemical measurements.CDOM absorption parameters from Riverine waters, Reservoir waters and Urban waters exhibited seasonal difference due to the terrestrial inputs.Referred to the risk formation theory of natural disaster, entropy evaluation method and DPSIR (force-pressure-state-impact-response) framework were coupled to establish hazard and vulnerability index.The overall ecosystem risk in this study area was focus on the regions of extremely, heavily and moderately vulnerable regions.