Three independent scientific lines of evidence were sought to determine the nutrient load limits to safeguard the macrophyte community of an intermittently closed and open lake/lagoon (ICOLL): (1) a literature review identified nitrogen load thresholds related to the collapse of macrophytes in similar systems in Australia, Europe and elsewhere, (2) an ICOLL expert carried out an assessment based on current local data and on data from 57 Australian coastal lakes and lagoons, and (3) a deterministic coupled hydrodynamic-ecological model was developed and applied to simulate the ecological outcomes of several nutrient loading scenarios. The three lines of evidence converged on well-defined nitrogen load estimates required to avoid the collapse of the macrophyte community. Uncertainties were slightly greater in relation to required phosphorus load limits, but the evidence still helped set a precautionary phosphorus load limit that accounted for these uncertainties. Thus, despite the challenges in setting load limits for complex ecosystems, multiple lines of evidence helped derive robust nutrient load limits for managing the ICOLL to safeguard values associated with a healthy macrophyte community.