A risk assessment process was used to trial the impact of potential new operating rules on the frequency of nest inundation for the White-throated snapping turtle, Elseya albagula, in the impounded waters of the Burnett River, Queensland, Australia. The proposed operating rules would increase the barrage storage level during the turtle nesting season (May-July) and then would be allowed to reduce to a lower level for incubation for the rest of the year. These proposed operating rules reduce rates of nest inundation by altering water levels in the Ben Anderson Barrage impoundment of the Burnett River. The rules operate throughout the turtle reproductive period and concomitantly improve stability of littoral habitat and fishway operation. Additionally, the proposed rules are expected to have positive socio-economic benefits within the region. While regulated water resources will inherently have a number of negative environmental implications, these potential new operating rules have the capacity to benefit the environment while managing resources in a more sustainable manner. The operating rules have now been enacted in subordinate legislation and require the operator to maintain water levels to minimize turtle nest inundation.