We used fuzzy cognitive mapping (FCM) to develop a generic shallow lake ecosystem model by augmenting the individual cognitive maps drawn by 8 scientists working in the area of shallow lake ecology. We calculated graph theoretical indices of the individual cognitive maps and the collective cognitive map produced by augmentation. There were a total of 32 variables with 113 connections in the collective cognitive map. The graph theoretical indices revealed internal cycles showing non-linear dynamics in the shallow lake ecosystem. The ecological processes were organized democratically without a top-down hierarchical structure. The most central variable in the collective map was submerged plants. The strongest connections were suspended solids concentration decreasing water clarity, phosphorus concentration increasing the phytoplankton biomass, higher water clarity increasing submerged plants, benthivorous fish biomass reducing submerged plants and increasing suspended solids concentration, and submerged plants decreasing suspended solids. The steady state condition of the generic model was a characteristic turbid shallow lake ecosystem. The generic shallow lake ecosystem model had the tendency to go into a turbid state since there were no dynamic environmental changes that could cause shifts between a turbid and a clearwater state, and the generic model indicated that only a dynamic disturbance regime could maintain the clearwater state. The model developed herein captured the empirical behavior of shallow lakes, and contained the basic model of the Alternative Stable States Theory. In addition, our model expanded the basic model by quantifying the relative effects of connections and by extending it with 22 more variables and 99 more weighted causal connections. Using our expanded model we ran 4 simulations: harvesting submerged plants, nutrient reduction, fish removal without nutrient reduction, and biomanipulation. Only biomanipulation, which included fish removal and nutrient reduction, had the potential to shift the turbid state into clearwater state. The structure and relationships in the generic model as well as the outcomes of the management simulations were supported by actual field studies in shallow lake ecosystems. Thus, fuzzy cognitive mapping methodology enabled us to understand the complex structure of shallow lake ecosystems as a whole and obtain a valid generic model based on tacit knowledge of experts in the field.