We have recently developed fish-based, multimetric indices for assessing and monitoring the health of the nearshore ( 2 m depth) waters of the permanently-open Swan Estuary, Western Australia. Here, we examine index scores calculated from fish community samples collected before, during and after two blooms of the harmful dinoflagellate, Karlodinium veneficum which have occurred in this system in the last decade. The historical (March 2004) and more recent (May 2011) algal blooms differed in their spatial extents, temporal persistence and severity of impact, and thus enabled us to assess the sensitivity of the estuarine health indices to ecological perturbations of differing intensities. The responses of these indices to the algal blooms confirmed that they are sufficiently sensitive to quantify ecological health responses to local-scale environmental perturbations, and to track the subsequent recovery of the system following their removal. In addition, the consistency of nearshore index scores across sampling occasions prior to the May 2011 bloom provides further confirmation that the nearshore health index is consistent and robust (i.e. is not overly sensitive to natural, background variability). Most interestingly, our results elucidate the avoidance movements of certain fish species and the vital role of nearshore habitats in this system as refugia for fish during severe algal bloom events. These indices, which are the first such tools to be developed for Australian estuaries, provide managers with a reliable and cost-effective, quantitative method for assessing and communicating the health of the Swan Estuary, and potentially of other estuaries across south-western Australia
