I investigated the effects of successional stage and micro-elevation on seedling establishment of Calophyllum brasiliense (Clusiaceae), a common canopy tree of seasonally flooded lowland forest along the Manú River meander zone in southeastern Peru. To compare seedling establishment between microhabitat types, I planted C. brasiliense seeds in a fully crossed experimental design of three successional stages (early, mid, and mature) and two micro-elevations (levees and backwaters). Seedling establishment success in this study was affected by both successional stage and micro-elevation, but micro-elevation was most important in mid-successional habitats. In general, seedlings in early succession experienced better conditions than in mature forest; light levels were higher, herbivory lower, and seedling growth higher. In mid-successional forest, micro-elevation determined habitat quality; backwaters had higher light levels, lower herbivory, and higher seedling growth and survival than levees. Mid-successional backwaters were similar in quality to early successional forest for seedling establishment, while levees in that same successional stage were the poorest microhabitats for establishment. Although mid-successional backwaters are similar to early succession for seedling establishment, in the long run, seedlings that establish in mid-succession have a lower chance of reaching reproductive size before their habitat ages to mature forest than members of their cohort that established in early succession. I hypothesize that successful recruitment for C. brasiliense in the Manú River meander system requires dispersal to early successional habitat.