[Truncated abstract] Most of Australia, and large areas of many other continents, is drained by intermittent rivers and streams, however comparatively few biogeochemical studies have been completed for these systems. Intermittent, dryland streams are highly dynamic environments subject to unpredictable and sporadic flow. Natural disturbance from lengthy drought periods and sudden floods are typical for these systems. Without adequate baselines for natural disturbances, it is difficult to quantify other effects from anthropogenic disturbance such as dewatering, land clearing, and urbanisation, or climate change. This thesis presents work from a four-year study examining the biogeochemistry of nitrogen (N), phosphorus (P) and carbon (C) in soils and sediments of two intermittent streams (Barnett Creek and Pirraburdoo Creek) in the Pilbara region of north-west Australia. The Pilbara is an area of ancient geology and highly weathered environments that is undergoing rapid development yet is poorly understood from an ecological perspective. The principal objectives of this thesis were to determine: i) how flooding affects the spatiotemporal patterns of nutrients in intermittent stream landscapes; ii) the role of flooding in N and C mineralisation and microbial dynamics; and iii) the connections between benthic algae, microbes and nutrient availability in channel sediments. To address these objectives, three field studies and two incubation experiments were conducted. Field studies at Barnett Creek indicated that flooding reduced the spatial heterogeneity of available soil nutrients and microbes in the stream landscape, and that topography (relative elevation) in the stream landscape was of less importance in influencing nutrient and microbial patterns than flooding or landscape position. ... Field studies at Pirraburdoo Creek indicated that microbial biomass and activity increased in benthic algal mats during mat senescent stages, and decreased after flooding when mat biomass peaked. Benthic algae grew rapidly in gravel run environments after flooding, while declining in pools, and demonstrated moderate N limitation and strong P limitation. Pools had two to eight times greater NO3-N, three to five times more total N, and two to three times more labile P, OC and total C than either pools after flooding, or runs before or after flooding. Hence, the pools at Pirraburdoo Creek represented a local, interflood store of nutrients in otherwise nutrient-poor landscape, when connectivity to upstream reaches or upland environments was weak or non-existent. This thesis provides the first detailed analysis of soil and sediment biogeochemical responses to flooding for intermittent streams in the Pilbara region and for semi-arid Australia. Further pressing questions raised by this work include: What is the key pulse size and frequency for maintaining Pilbara riparian communities as well as soil microbial function? How do the spatio-temporal nutrient and microbial patterns observed persist over (i) multi-decadal scales, (ii) mega-spatial (larger landscape to regional) scales, (iii) different flood frequency-magnitude regimes, and (iv) different stream sizes? Stream biogeochemistry is a burgeoning field, and it is therefore reasonable to expect such existing gaps in knowledge may be addressed in the near future.