Integration of new methodologies in monitoring native fish habitat and populations in the southwestern U.S.

Native fish populations and their habitats are declining in the southwestern United States. The upper Verde River (UVR) is one of a shrinking number of remaining perennial stream systems where multiple populations of native fish species still exist. This study utilized unoccupied aerial vehicle (UAV), terrestrial lidar, real-time kinematic (RTK) survey technology and environmental DNA (eDNA) sampling to assess current riparian and in-stream habitat conditions and compare them to an assessment conducted in 2009 to assess current suitability and long-term trends in populations and habitat conditions of native fish. Average stream discharge within the UVR has fallen over 40%, from a high of 30.6 cubic feet per second (cfs) in 1995 to recent lows in 2023 of just over 18 cfs. Woody vegetation cover has increased within the riparian zone by approximately 30% since 2007 and cattail backwater areas, which support non-native fish and amphibian populations, now comprise nearly 9.4% of total riparian cover after being nearly absent in 2007. Analysis of eDNA fish samples suggest that populations of all native fish species are no longer detected within the first 10 km (kms) of the river, with Spikedace (Meda fulgida) appearing to have been extirpated from the UVR. Groundwater pumping in the upper watershed along with recent long-term drought conditions are most likely associated with the decline in baseflow and are resulting in the expansion of deep-rooted woody species and cattails along the streambanks, confining the stream channel and reducing suitable habitat for native fish species.