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A dynamic (time dependent) mathematical model of the monthly cycling of suspended particulate matter (SPM) in lakes with variable water levels has been developed. The model has been applied for the large subtropical Lake Kinneret (Israel), which has variable water levels related to domestic freshwater needs and climatological conditions. The main conclusions from this work are: 1. Uncertainty analyses (Monte Carlo simulations) have shown that the two most important model uncertainties concern sedimentation and erosion related to a lowering of the wave base (=the water depth separating areas where discontinuous and continuous sedimentation of fine matter occurs). The best way to improve the reliability of the mean monthly SPM-predictions would be to improve the modelling parts related to sedimentation and a lowering of the wave base. All other processes are of less importance for the SPM-predictions (e.g. inflow, outflow, primary production, resuspension, mineralization and mixing). 2. A successive, gradual lowering of the wave base seems to correspond to the ‘worst case’ scenario likely to alter SPM-values the most. 3. In the ‘worst case’ scenario, very high levels of SPM may be maintained for a long time (>10 years), which would likely cause serious changes to the Lake Kinneret ecosystem. These results indicate the existence of a narrow threshold range of artificial changes of lake morphometry (water level lowering of about 4–5 m from the maximum water level), which may cause significant deterioration of water quality in Lake Kinneret.