Predictions occupy a central position in environmental management. To make predictions, models are constructed and analyzed. In this framework the quantitative approach based on large simulation models dominates. It has been shown in various ecological contexts that relevant aspects of the system's behavior may depend on the structure of the interactions. In this paper a strategy to reconstruct the structure of a freshwater ecosystem is presented. It uses statistical patterns and field observations combined with a qualitative algorithm, that of the loop analysis. This procedure leads to unambiguous conclusions about system structure, although alternatives are possible. The models obtained are then qualitatively investigated and results discussed about management opportunities.