This paper presents a Qualitative Reasoning model of the algal bloom phenomenon and its effects in the Danube Delta Biosphere Reserve (DDBR) in Romania. Qualitative Reasoning models represent processes and their cause-effect relationships in a flexible and conceptually rich manner and as such can be used as instruments for capturing and sharing explanations of how systems behave. The DDBR model is based on expert knowledge and captures the main factors contributing to the dynamics of this aquatic ecosystem. Focal points of the model are the relationships between temperature, water pollution from the Danube catchment area, and cyanotoxins. These factors gravely affect aquatic biota and ultimately human wellbeing. In addition to capturing domain knowledge, this paper discusses solutions for representing typical patterns in ecological systems using Qualitative Reasoning techniques.