Deep hooking is one of the key causes of mortality among angled-and-released teleosts worldwide. We assessed the effects of natural baits and other variables on the frequency of deep hooking and postrelease mortality in two Australian native freshwater fishes that are classified as vulnerable or endangered: Golden Perch Macquaria ambigua and Freshwater Catfish Tandanus tandanus. Sixty-one angled Golden Perch were released and monitored in individual submersible cages at their capture location or were held in shore-based group tanks; of these fish, 97% were hooked with natural baits, 41% were deep hooked and had their lines cut, and 44% died. Of the Golden Perch that died, 70% were deep hooked, and hook location and two associated factors (hook removal and ease of handling) were identified as significant predictors of mortality. Mortality of Golden Perch was also significantly greater during the afternoon session on the first day of angling than during other sessions and days. In contrast, of the 98 Freshwater Catfish that were similarly angled with natural baits, only 9% ingested hooks and only 3% died, with no significant mortality factors identified. None of the control fish died. Interspecific differences in deep-hooking frequency are discussed in relation to the significant influences of time of day (both species), angler experience (Freshwater Catfish), and river reach (Golden Perch) and the likely differences in mouth morphology and feeding mechanisms. The results indicate that anglers should refrain from using natural baits when fishing for Golden Perch so as to minimize deep hooking and postrelease mortality, which will ultimately help conserve and manage these stocks.