Different types of rivers have their own ecosystems. Based on the laden-starved sediment content in rivers, they can be classified as sediment-laden turbid (SLT) and sediment-starved clear (SSC) river ecosystems. Understanding the evolution process and driving factors of these two river ecosystems is very important for the protection of their ecology. Until now, however, there has been no comprehensive study that integrates biological and nonbiological factors in river ecosystems. Here, the self-organizing feature map (SOFM) model based on the maximum generalized entropy principle can integrate the two and conduct research on the evolution of river ecosystems. First, we can evaluate the stabilities of the SLT river ecosystem (i.e., the Weihe River mainstream) and the SSC river ecosystem (i.e., the Weihe River tributaries at the northern foot of the Qinling Mountains). Second, the degree of influence of various factors on stability was assessed. Finally, correlation analysis was added to study the driving relationship between the internal and external aspects of the ecosystem. The results showed that the stability of the SLT river ecosystem (mean value 3.371) was lower than that of the SSC type (mean value 5.343). However, the SSC river ecosystem was more susceptible to being affected because more factors could affect its stability. Further study indicated that although turbidity was the largest connection weight in the two river ecosystems, the reasons for its increase were different. This result was due to the increased sediment content in the SLT river ecosystem and the growth of algae in the SSC ecosystem. The main reason for this difference was that the SLT and SSC river ecosystems had different external driving forces. The SLT river ecosystem was mainly driven by land utilization, and the SSC was mainly driven by hydrological situations and climate factors. Although there are differences between the two ecosystems, they may transform into each other when the external driving force of the river ecosystem changes. This study emphasizes the importance of external background to the evolution trend of river ecosystems and the difference in the influence of internal factors on the stability of river ecosystems.