One of the rarest birds in the world, the Madagascar Pochard Aythya innotata was thought to be extinct until a small population was found in 2006. Little is known about this diving duck as it had not been studied prior to its decline and disappearance. Its rediscovery provided the opportunity to study this species in the wild for the first time and to assess the viability of this last remaining population. The population is small, fluctuating around 25 individuals, and mainly utilises two small volcanic lakes in the far north of Madagascar. Nesting occurs on only one of these lakes, Matsaborimena. Nest success (76% in 2007–2008) and hatching success (89% in 2007–2008) are both comparable to other Aythya species, but fledging success (4% in 2011–2012) is extremely low. Duckling mortality rates peak between 14 and 21 days old. We propose that starvation is the major cause of duckling mortality. Examination of faecal samples and stable isotope analysis of feathers and potential food items provide evidence that adult pochards are insectivorous, favouring caddis fly larvae. Macroinvertebrate density in the benthos of Matsaborimena is low. Adults spend 38% of daylight hours foraging, mainly in the shallowest water. However Matsaborimena is steep-sided and has no areas shallow enough for diving ducklings to feed. We conclude that these lakes are not good breeding habitat for this species. The Madagascar Pochard’s persistence here and not at other sites is probably due to a lack of the human-induced habitat degradation that has impacted many other wetlands in Madagascar.