A decision support tool has been developed to assist with managing Ruppia beds and maintaining the biological diversity of Waituna Lagoon. The results from this tool are presented as outputs from model simulations of physical, chemical and biological variables within the lagoon. Input data for the model simulations were adjusted to simulate sensitivity of the model to (i) input data quality and quantity, (ii) complexity and formulations used in the model itself, (iii) parameters used to adjust physical and biogeochemical environmental responses in the model, and (iv) potential management options. Parts i-iii were necessary to assure a level of confidence in the model so that part iv, the management options, could be used to provide a basis for what might be required to sustain persistent, productive Ruppia beds in the lagoon.