A modified abstract version of the Comprehensive Aquatic Simulation Model (CASM) is found to exhibit three types of folded bifurcations due to nutrient loading. The resulting bifurcation diagrams account for nonlinear dynamics such as regime shifts and cyclic changes between clear-water state and turbid state that have actually been observed in real lakes. In particular, pulse-perturbation simulations based on the model presented suggest that temporal behaviors of real lakes after biomanipulations can be explained by pulse-dynamics in complex ecosystems, and that not only the amplitude (manipulated abundance of organisms) but also the phase (timing) is important for restoring lakes by biomanipulation. Ecosystem management in terms of possible irreversible changes in ecosystems induced by regime shifts is also discussed.