Rivers in arid Australia only flow intermittently so long-lasting waterholes are critical locations for aquatic life. Knowledge of the location and basic character of waterholes should underpin catchment scale condition assessment and associated ecological understanding.  Across the Lake Eyre Basin, waterhole monitoring is conducted to assess river health, however, in the Finke River poor mapping was a barrier to interpreting monitoring data. Work to address this knowledge gap in the mid-section of the Finke combined consultation with pastoralists and traditional owners, inspection of satellite imagery, aerial survey and ground survey. Only 20 waterholes were previously mapped; all of undocumented character. Information from landholders convinced us that 3 waterholes are permanent, but that relatively few others lasted more than a year without flow. Aerial survey 15 months after a flow event identified 274 distinct pools. Ground survey indicates most were shallow (< 1m) but with depths ranging up to 9 m deep. Water levels in many pools were surprisingly close to cease-to-flow level, and the majority of pools were saline, consistent with a significant groundwater influence. All 9 Finke fish species were present. The mid-Finke is now considered to be as important as the rocky headwaters in sustaining the fish fauna, with many pools that only dry out in major droughts (e.g. >2 years without flow). The abundance and diversity of long-lasting waterholes both help explain why the Finke has a higher diversity of fish than other isolated arid zone rivers. The results also demonstrate the importance of adequate wetland inventory.