In this study, we explore the potential contributions of a risk perception framework in understanding public perceptions of unstable ecosystems. In doing so, we characterize one type of common ecological risk– harmful algal blooms (HABs)–in four of the most seriously eutrophicated freshwater lakes in China. These lakes include Chaohu, Dianchi, Hongze, and Taihu, where a total of 2000 residents living near these sites were interviewed. Regional discrepancies existed in the pilot study regarding public perceptions of ecological changes and public concerns for ecological risk. Comparing HABs and other kinds of risks (earthquake, nuclear, and public traffic) through the psychometric paradigm method, Knowledge, Effect, and Trust were three key factors formulating the risk perception model. The results indicated that Knowledge and risk tolerance levels had significant negative correlations in the higher economic situation while correlations in the lower economic situation were significantly positive. Effect and risk tolerance levels had significant negative correlations in the high and middle education situation while correlations in the low education situation were close to zero or insignificant. For residents from Taihu with comparatively higher economic and educational levels, more investment in risk prevention measures and stronger policies are needed. And for residents from Hongze and Dianchi with comparatively low economic and educational levels, improvement of the government’s credibility (Trust) was the most important factor of risk tolerance, so efforts to eliminate ecological problems with the stepwise development of economic and educational levels should be implemented and gradually strengthened. In turn, this could prevent public discontent and ensure support for ecological protection policies.