The Cape Sable seaside sparrow (Ammodramus maritimus mirabilis) is Federally protected under the Endangered Species Act of the United States of America. This legislation prohibits direct or indirect take - the killing or harming - of the protected species. In 1993 and 1995, the opening of floodgates into Everglades National Park during the normal dry season resulted in a direct take of the sparrow. The argument was also made that there was indirect take through destruction of the habitat upon which the sparrow depends. Using a combination of fieldwork and satellite image analysis, we show that the floods did damage to the habitat of the sparrow. Moreover, they did so for a period longer than the actual flooding, further increasing the sparrow's extinction risk. Recovery of the sparrow population to pre-flood levels will require an adequate and stable amount of habitat. We now have a technique for monitoring that habitat and ensuring that poor water management does not threaten it. More broadly, this technique has the potential for monitoring the habitat of many other species and avoiding another situation such as the sparrow faces.