The Cayumapu River's black-necked swan population in southern Chile lost its main dietary item, Egeria densa, during an environmental crisis which occurred in 2004 in the Carlos Andwanter Nature Sanctuary. The main goal of this study was to test the effect of diet on the physiologic response to this new ecologic challenge. The results revealed that the new diet of this population was composed primarily of roots and sedimentary microalgae, with chemical and energetic content similar to the diet of the control population. Nevertheless, the mean body mass of the Cayumapu River swans was 25% lower than that of control birds. In addition, the biochemical and hematologic profiles of the study population were indicative of malnutrition and a hyperferremic, hyperphosphatemic, and lymphopenic condition. Liver enzyme activities did not support that the malnutrition was a secondary consequence of liver dysfunction, as is expected under hemochromatosis or environmental toxics exposure.