This PhD thesis focuses on the basic eco-hydromorphic dynamics of pristine tropical stream systems on the island of Borneo. Exploring theories and models developed in temperate streams and rivers to determine if they can be applied or appropriately adjusted to describe and explain some of the tropical stream processes. Streams in Ulu Temburong National Park in Brunei Darussalam are used as a case study owing to its pristine rainforests and intact stream catchments that have hitherto been little studied. The first part of the thesis assesses the distribution of macroinvertebrates in flow biotopes and investigates if the arrangement, structure and juxtaposition of the flow biotopes influences macroinvertebrate assemblages and population. It is demonstrated that the more consistent environmental conditions of waterfalls and cascades, in comparison to the mixed-substrate biotopes (pools and riffles), have a strong influence on the macroinvertebrate communities. The influence of discontinuity on stream biota and ecosystem functions was explored at confluences zones and in pools above-and-below waterfalls. Results suggested there was a stronger link between confluence hydrology and macroinvertebrates, than with organic matter and periphyton. The waterfall study found varied effects of biotic and abiotic factors on community structure and ecosystem function. Higher fish densities were in below-waterfall pools and higher shrimp abundance in above-waterfall pools. However, macroinvertebrate densities (excluding shrimp) were similar among both pool types. Ambient periphyton was higher in below-waterfall pools but leaf litter decomposition rates did not differ, suggesting that neither shrimp nor fish densities had consistent impacts on this ecosystem function. The trophic structure of the macroinvertebrates living on waterfalls was investigated using stable isotope analysis (SIA; δ13C and δ15N of leaf litter and periphyton) and gut contents analysis (GCA), establishing potentially three trophic levels. This thesis successfully used models developed in temperate streams to develop an understanding of the basic dynamics of pristine tropical stream systems in terms of eco-hydromorphology, which will assist with sensible conservation management and for robust ecosystem monitoring.