The Niobrara NSR monitored the threatened piping plover and endangered least tern from 2001 to 2006. An eastern portion of the scenic river stretch was designated as critical habitat for these birds. A yearly census was taken, and nest monitoring, egg floating (aging), nesting success and other parameters were noted. In 2007 the NPS adopted a less invasive approach and does an annual adult census, locates nesting colonies and notes nests and number of eggs.
Other listed plants and animals include the river otter (state threatened), whooping crane (federally endangered), American burying beetle (federally endangered), finescale dace (state threatened), northern long-eared bat (federally threatened), and northern redbelly dace (state threatened).