The hydrologic, geomorphic, and ecological dynamics of tropical montane streams are poorly understood in comparison to many temperate and/or alluvial rivers. Yet as the threat to tropical freshwater environments increases, information on the dynamics of relatively pristine streams is important for understanding landscape evolution, managing and conserving natural resources, and implementing stream restoration. This dissertation characterizes the geomorphology and hydrology of five adjacent watersheds draining the Luquillo Experimental Forest (LEF) in northeastern Puerto Rico, and discusses implications on aquatic habitat. I performed several interrelated studies, including: 1) formulating a geographic information systems (GIS) framework to estimate hydrologic parameters from topographic information and hydrologic records, 2) developing a method to determine active stream channel boundaries (“bankfull” stage) that allows for comparison of channel geometry on the basis of flow-frequency, 3) decoupling the relative influences of lithologic and hydraulic controls on channel morphology using an extensive field-based stream survey and analysis of stream profiles, channel geometry, and sediment dynamics, 4) linking network- and pool-scale geofluvial dynamics to the abundance of migratory fish and shrimp through a collaborative analysis combining geomorphic surveys and aquatic faunal sampling. This research indicates that these streams have some properties resembling both temperate montane and alluvial rivers. Similar to low-gradient rivers where floodplains mark channel boundaries, the active channel stage in these streams is defined by the incipient presence of woody vegetation and soil development. Systematic basin-scale geomorphic patterns are well-developed despite apparent non-fluvial and lithologic control on local channel morphology. This implies that strong fluvial forces are sufficient to override channel boundary resistance; a feature common in self-forming “threshold” alluvial channels. Migratory aquatic fauna abundances are influenced by a variety of geomorphic factors such as barrier waterfalls and suitable headwater habitat, and are consequently highly variable and patchy. These results stand in contrast to the notion that aquatic communities mirror systematic geomorphic gradients, but rather acknowledges the influences of multiscale geomorphic processes. Ultimately, this research provides baseline information on physical and biological processes in relatively unaltered tropical streams and can be used to inform further studies that document human interactions with stream networks.