Reduced nest survival due to anthropogenic changes contributes to bird population declines. Understanding the drivers of nest failure can thus identify targets for conservation. Nest failure is shaped not only by ecology, but also by behaviour, especially in species with complex social systems. However, the relative importance of behavioural and ecological processes, alone or in interaction, can be hard to quantify, particularly when multiple threats to nest survival co-exist. We examined the fates of 859 nests (31% survived) of Endangered purple-crowned fairy-wrens (Malurus coronatus coronatus). This cooperatively breeding species inhabits waterways in the monsoonal savanna of northwest Australia and is an indicator of the health of threatened but biodiverse riparian ecosystems. We determined the effects of habitat quality (density of Pandanus aquaticus, the dominant midstorey vegetation in this system), weather, and social group size on competing risks to nest survival using a multinomial logistic-exposure model (13,179 exposure days over 17 years). High-quality habitat correlated with lower predation risk (48.4% of all nests were depredated). Furthermore, although proximity to water correlated with a greater risk of flooding (15.3% of all nests were flooded), this effect was attenuated by habitat quality. Nest abandonment was unrelated to ecology or behaviour. Social behaviour also reduced predation risk. Nests of larger social groups experienced less predation than those of unassisted pairs or smaller groups, especially during the nestling stage. This indirectly magnifies the positive effect of habitat quality, as higher-quality habitat supports larger groups. Riparian ecosystems in tropical savannas are important biodiversity refuges from current and future hot and dry conditions. Poor management of fire and grazing reduces habitat quality, and we show that poor riparian habitat quality is associated with reduced nest survival through predation and flooding. To support purple-crowned fairy-wrens and other socially and/or ecologically similar species that rely on these ecosystems, conservation management actions should aim at improving not only the extent but also the quality of riparian habitat and preserving existing areas of high P. aquaticus density.