1. Network theory offers new perspective on movement data by evaluating the relationships between animal movements (links) and detection locations (nodes) in spatially complex systems, including human-altered landscapes. 2. We applied network analyses to intra- and interspecific movement patterns in the migration behaviour and dam passage success of two anadromous fish species, Pacific lamprey Entosphenus tridentatus Gairdner and Chinook salmon Oncorhynchus tshawytscha Walbaum, when moving through a large multi-fishway hydroelectric project (Bonneville Dam, USA). 3. Network analyses revealed greater variation in movement for Pacific lamprey compared with Chinook salmon. Salmon that passed the dam had networks consisting of more direct passage routes with fewer overall movements compared with lamprey that passed the dam. Lamprey that did not pass the dam exhibited a wide range of behaviours, from approaching only one fishway site to testing all possible passage routes. Accounting for the time spent in the network improved the ability to detect biological differences in network structure for lamprey that did and did not pass the dam. 4. The movement patterns likely resulted from different behavioural responses to complex environmental and internal factors affecting a philopatric species (Chinook salmon) versus a non-philopatric species (Pacific lamprey) when moving through an engineered environment designed primarily for salmon. 5. Synthesis and applications. Our case study highlights the potential for network analyses to link questions of basic movement ecology with monitoring of movement and behaviour in human-altered landscapes. Network analyses can thus serve as a valuable tool for describing movement and behaviour in the face of environmental change and assessing the effectiveness of mitigation efforts at spatially complex obstacles to animal movement.