SummaryA species recovery project for the endangered fish Red‐finned Blue‐eye (Scaturiginichthys vermeilipinnis) commenced in 2009 at Edgbaston Reserve in central western Queensland. To date, the project has included relocations and control of alien Eastern Gambusia (henceforth Gambusia, Gambusia holbrooki), using the piscicide rotenone. Preventing Gambusia colonising springs where Red‐finned Blue‐eye occur or have been relocated is crucial to the success of the project. As such, this study tested the use of porous silt fences that were installed around five springs from 2012. Results indicate that silt fencing is a suitable barrier material and that provided installed silt fences are serviced regularly, the material is an effective method of quarantining populations of endangered species in isolated aquatic environments. Four of the five installed fences were effective, and maintenance consisted of small repairs at regular intervals (quarterly) followed by replacement after 2 years. As such, silt fencing may have wider application in the conservation of endangered fish and other organisms, particularly in areas where isolated waterbodies occur and where their size renders exclusion fencing a practical recovery action.