Regional transportation development (RTD) is an important stressor of urban agglomeration ecosystems. Groundwater recharge potential may be adversely affected when natural soil is replaced by impervious materials. To systematically identify the urban agglomeration ecological risk (UAER) of RTD in the southern Fujian Golden Triangle, water regulation was used as an assessment endpoint, and RTD was considered the stressor. We used the Soil Conservation Service Curve Number method (SCS-CN) to analyze the internal relationship between the assessment endpoint and the stressor factors. Then, a multi-level risk characterization method was used to show the evolutionary process of risk, and to provide a scientific basis for the management of UAER. Based on the current RTD plan, the UAER assessment shows that there is a 0.90 probability of that the risk distribution results will occur by 2030. The intensity of stress from arterial roads on the urban agglomeration ecosystem is greater than that of the railway system. By considering the development of the railway system as a factor in the stress of RTD, this study of UAER assessment differs from past studies of urban ecological risk assessment, since the latter considers only highways. We also propose a systematic method of risk assessment simulation-prediction.