We compiled electrofishing and habitat data sampled from 1990 to 2019 in the Harney Basin by the US Geological Survey (USGS), Oregon Department of Fish and Wildlife (ODFW) and the High Desert Partnership (HDP) to describe native and non-native fish distributions and their habitat associations. USGS collected eDNA data in 2019 to refine the known distributions of common carp (Cyprinus carpio). Site
eDNA-based spatiotemporal distribution data (occupancy model format) for rainbow trout (Oncorhynchus mykiss) and bull trout (Salvelinus confluentus) within the Bruneau-Jarbidge Rivers Wilderness in southern Idaho and northern Nevada, USA. Data also include stream discharge and stream temperature data for each site. All data were collected between October 2015 and September 2016.