A common strategy used to conserve turtles is to increase the number of hatchlings entering the population by protecting the nests. Typically, nest protection programs require regular and systematic abundance surveys conducted over lengthy periods between oviposition and sexual maturity (20+ years) to assess if this conservation strategy is effective in recovering the population. Here, we describe a methodology that dramatically reduced the monitoring period (3 years) required to assess the impact of nest protection upon a threatened freshwater turtle (Elusor macrurus). An age-at-length curve was developed to define the size of turtles produced within the nest protection program period (15 years) and mark-recapture models were used to compare population demographics between areas with and without a nest protection program. Unexpectedly, the study revealed substantially fewer turtles younger than 15-years of age in areas with nest protection compared to areas where no nest protection program existed. The reason for the lack of recovery was due to a significantly lower number of nesting females and a much lower rate of survival from hatching through to the sub-adult stage within the area of the nest protection. Consequently, for E. macrurus, the nest protection program did not result in localised population recovery and in-stream mortality may be an equal if not greater threat to E. macrurus in this part of their geographical range. The study presents a relatively rapid methodology to assess the effectiveness of turtle nest protection programs and diagnose the reason for ongoing population declines.