Amphibian conservation studies often rely on auditory call surveys to determine distribution, abundance, and habitat associations of anuran species. Call surveys omit important life stages, however, and conservation recommendations from call surveys alone risk creating population sinks or ecological traps. To more effectively determine the effects of a catastrophic flood on an amphibian community, we surveyed tadpoles and metamorphs of six anuran species in the Missouri River floodplain in 2012 and 2013. Inference gleaned from these surveys was compared to inference from previous work with call surveys. For 8 of 10 species-years, extinction probabilities were >0 for tadpole and metamorph stages, indicating there may be habitat factors affecting tadpoles and metamorphs beyond those affecting calling adult males. In several cases we discovered habitat associations for tadpoles and metamorphs that were not present during call surveys. We had previously recommended shallow slopes for Blanchard's Cricket Frog, but we found slopes that were too shallow were detrimental for metamorph emergence. Woodhouse's Toad metamorphs had opposite preferences for slope than adults and preferred larger wetlands with less emergent vegetation. Gray Treefrog tadpoles had preferences for emergent vegetation that differed from adult requirements. Our work highlights the need to consider habitat factors affecting life stages beyond calling adult males. Amphibian conservation and management should proceed with sufficient information on critical aquatic life stages.