Constructing community fruit–frugivore networks has proved challenging in tropical forests to date, particularly in lowland Amazonia, which hosts the most diverse spectrum of frugivorous vertebrates and morphological fruit types worldwide. We assessed data on fruit resource production, frugivore assemblages and corresponding fruit–frugivore networks in two contrasting forest types along the Rio Juruá of western Brazilian Amazonia: seasonally flooded várzea (VZ) and unflooded terra firme forest (TF). Over 2 y we conducted monthly surveys of fruit patches and medium- to large-bodied vertebrate frugivores within three 100-ha plots (two TF, one VZ), supplemented by fruit surveys along 67 5-km transects distributed across two contiguous forest reserves (41 TF, 26 VZ). Observations of trophic interactions were supplemented by semi-structured interviews with experienced hunters and fishermen from 16 local communities. The resultant binary networks contained low proportions of all potential interactions (TF: 25.7%, VZ: 19.4%) between 36 functional groups of frugivores and 152 plant genera and, while we report significant heterogeneity in fruit resource use among broad frugivore guilds within each forest type, recursive partitioning analysis failed to clearly match differences in fruit selection to fruit traits. The annual flood pulse in várzea forests had an overriding influence on the species turnover of both fruit resources and frugivores between the two forest types, with higher-order effects on network structure.