Hydraulic lock structures have been used for hundreds of years to control and maintain water levels in waterways. The most common are gated water regulation structures used to catch and divert water, and form an essential and critical part of many flood control and agricultural schemes. Although there are clear economic advantages to building the structures, they can contribute to major water quality problems for the waterways they influence (i.e. increased residence times and a change in mixing ability). Further, in most cases, the methods previously used to assess how the structures and their operations influence the flow regimes between the two connected systems were limited, thus hydraulic designers rely on simple formulations, existing literature and experience. Consequently, the objectives of this thesis were to undertake a detailed field study and develop a methodology and computer simulation tool to calculate the flow through a hydraulic structure connecting two water bodies so that future designs can be undertaken based upon sound knowledge. To demonstrate the outcomes of this thesis, the methodology and model were applied to an existing hydraulic structure (referred to as Structure C). Structure C is used to connect and exchange water between the tidally dominated section of the Nerang River estuary and an artificial lake system (Burleigh Lakes) on the Gold Coast, Australia. The gates of this structure open four times each day (once during each semi-diurnal tidal phase) and remain open for a period of 2 hours, allowing alternative and partial exchange between the two water bodies. To gain a better understanding of the dynamics of each waterbody under the influence of the structure, a series of detailed field experiments were initially undertaken to understand and quantify the exchange of water and its mixing ability. Tide gauges deployed within the lake indicated a water level change during each opening of up to 22 cm, equating to 413,600 m3 of water entering the lake over the 2 hour discharge period. Salinity profiles showed that the structure permitted the exchange of saline and freshwater between the two systems, during each tidal cycle, in turn maintaining the lake system as a saline (brackish environment). However, the field study also revealed that the controlled exchange of water between the systems perpetuated a permanently stratified environment on both sides of the structure. To simulate the flow dynamics influenced by Structure C, new routines were incorporated into an existing hydrodynamic model (BFHYDRO) within the model's grid and computational code, as part of this thesis. To achieve this, the flow in and out of the hydraulic structure cell (used to represent the hydraulic structure's location within the model grid) was calculated entirely from the local water level gradients on either side of the structure at each time-step, and not prescribed. This was found to be essential for complex tidally-dominated systems, such as the Nerang River. Routines were also developed to replicate the opening and closing times of the gates. Following the development of the methodology, the hydraulic structure cells were tested and applied to simulate the flow through Structure C and the complex exchange between the estuary and lake, in 2 and 3-dimensions. Tests indicated that the opening and closing times of the gates and the calibration of the discharge coefficient (which forms part of the broad-crested weir formula) were the most sensitive parameters to ensure the correct volume of water exchange between the two systems. Statistically, the model-predicted results compared very well with available surface elevation data within the estuary and lake, and thus, quantified the ability of the hydraulic structure cells to simulate the flux between the estuary and lake for each opening. Following the model validation process, results from the existing configuration were compared with hypothetical design alternatives and are documented herein. Further, part of the thesis also explored a practical and effective computer based learning strategy to introduce and teach hydrodynamic and water quality modelling, to the next generation of undergraduate engineering students. To enhance technology transfer a computer based instructional (CBI) aid was specifically developed to assist with the setup, execution and the analysis of models' output, in small easy steps. The CBI aid comprised of a HTML module with links to recorded Lotus Screen cam movie clips. The strategy proved to be a useful and effective approach in assisting the students to complete the project with minimum supervision, and acquire a basic understanding of water quality modelling. Finally, it is anticipated that this new modelling capability and the findings detailed herein will provide managers with a valuable tool to assess the influence of these structures on water circulation for present and future operations within the region. This model can also be set up at other sites to pre-assess various design configurations by predicting changes in current flows, mixing and flushing dynamics that a particular design might achieve, and assist with the selection process before the final selection and construction.