Cereal nitrogen-use efficiency (NUE) in developed and developing countries stands at 42 and 29% respectively. In Australia wheat NUE stands at 41% with the remaining 59% potentially contributing to environmental and health concerns. Processes such as ammonia volatilization, nitrification, leaching, erosion, runoff and denitrification account for 92% of nitrogen (N) loss from the plant-soil system. Achieving synchrony between N supply and crop demand is key to optimizing trade-offs among yield, profit and environmental protection in both large- and small-scale farming systems. Using enhanced-efficiency fertilisers such as controlled-release fertilisers (CRFs) may be one option to obtain a marked improvement in NUE in cereals. While soil moisture plays a significant role in plant growth and development, excessive soil moisture can cause significant yield losses. Waterlogging is a major abiotic constraint to cereal production in the high rainfall zones of Australia, particularly in areas with duplex soils. Understanding how we can improve cereal yield and NUE particularly under waterlogged conditions could help increase crop productivity. This research sought to address three key research questions namely: (a) can timing of N application and source of applied N alleviate the adverse effects of waterlogging on wheat and barley growth and physiology; (b) can CRFs improve wheat yield, NUE and their components under waterlogged conditions; and (c) is the uptake of NH4\\(^+\\) along the root axis of selected wheat and barley varieties under hypoxia significantly higher than NO3\\(^-\\)? These questions were answered through studies under glasshouse and field conditions as well as laboratory experiments. Under glasshouse conditions, identified waterlogging sensitive wheat (cv. Mackellar) and barley (cv. Naso Nijo) varieties treated with conventional urea and a CRF were waterlogged for 35 days and allowed to recover for another 35 days. During the study, leaf chlorophyll content and chlorophyll fluorescence were recorded on a weekly basis. Tiller number, green leaf area, above-ground dry matter (AGDM) and root DM were determined after waterlogging and recovery. In the field, the experiment was designed as a split-plot with irrigation regime and N fertiliser application as main-plot and subplot factors with three replicates. The irrigation regime included: rainfed, irrigated and waterlogged while N fertiliser application had nil N, single-applied urea, split-applied urea and CRF treatments. Nitrogen fertiliser was applied at a rate of 90 kg N/ha and piezometers were randomly installed to monitor the depth of the water table. Wheat growth and yield attributes including leaf area, leaf area index (LAI), tiller number, ear number, grain yield, AGDM, thousand grain weight (TGW) and harvest index (HI) were determined at specific growth stages namely: stem elongation (GS32), anthesis (GS61) and maturity (GS92). NUE, its components: nitrogen uptake efficiency (NupE) and nitrogen utilisation efficiency (NutE), N harvest index (NHI) and grain protein content (GPC) were also determined. Mapping the uptake of NH4\\(^+\\), NO3\\(^-\\) and H\\(^+\\) under hypoxia involved measurement of steady-state net fluxes of NH4\\(^+\\), NO3\\(^-\\) and H\\(^+\\) ions of wheat cv. Revenue and barley cv. Naso Nijo main roots at different positions along the root axis using non-invasive microelectrode ion flux estimation (MIFE) technique. Under glasshouse conditions, the results showed that N fertiliser application improves leaf chlorophyll content, tiller number, green leaf area, AGDM and root DM during waterlogging and recovery. Differences between N treatments were evident with the CRF having the highest amount of AGDM for both selected wheat and barley varieties. Conventional urea on the other hand, improved wheat and barley growth at the start of waterlogging and significantly during recovery as the remaining urea was top-dressed. Under field conditions, the study findings showed a significant interaction between irrigation regime and N fertiliser application for tiller number (P = 0.013) and leaf area (P = 0.014) at GS32. The AGDM per plant was significantly affected by irrigation regime (P = 0.001) and N fertiliser application (P = 0.012) while AGDM per unit area was significantly affected by the irrigation regime only (P = 0.001). At GS61, the irrigation regime (P = 0.001) and N fertiliser application (P < 0.05) had a significant effect on the tiller number, ear number and AGDM per plant. There was no significant interaction between the irrigation regime and N fertiliser application (P > 0.05). At maturity, yield attributes including tiller number, ear number and grain yield were significantly affected by irrigation regime (P = 0.001) and N fertiliser application (P < 0.05). The CRF had the highest grain yield for all irrigation regimes with 9.2 t/ha, 9.4 t/ha and 6.8 t/ha for the rainfed, irrigated and waterlogged, respectively. The urea treatments had an average of 8 t/ha for both the rainfed and irrigated, and 5.3 t/ha for the waterlogged. NUE was significantly affected by irrigation regime (P = 0.001) and N fertiliser application (P = 0.036). The waterlogged plants had the lowest NUE for all corresponding N treatments under the rainfed and irrigated regimes. The CRF had the highest NUE for all irrigation regimes. Under waterlogged conditions, the CRF improved NUE by 17% and 27% more than single- and split- applied urea, respectively. No significant variations were observed between N treatments for components of NUE, NHI or GPC for the rainfed and waterlogged treatments. Laboratory studies showed that the uptake and efflux of NH4\\(^+\\) and NO3\\(^-\\) ions in wheat and barley varied significantly (`P` = 0.001) between different positions along the root axis at 20 ˜í¬¿M and 1 mM NH4NO3 during normoxia and hypoxia. Hypoxia increased the uptake of NH4+ and NO3- for both wheat and barley and there was a preference for NH4\\(^+\\) over NO3\\(^-\\). Genotypic differences between wheat and barley were evident, with wheat having the highest uptake of both NH4+ and NO3- for the control and hypoxia at 20 ˜í¬¿M and 1 mM. It was concluded that N fertiliser application could alleviate the adverse effects of waterlogging in cereals. Applying full amount of the required fertiliser at sowing helps plants to withstand the adverse effects of transient and intermittent waterlogging through enhanced vegetative growth. Top-dressing urea after waterlogging and the termination of waterlogging to allow recovery enhances plant growth and development. Using CRFs may improve cereal growth and NUE though there might be no significant yield advantage over conventional urea to warrant investment. The findings also highlight the dynamic process of N uptake during hypoxia, which is characterised by significant variations over relatively short distances and periods of time. Hypoxic conditions also seem to trigger mechanisms that mediate N uptake resulting in higher uptake rates.