Date of Award


Degree Type


Degree Name

Doctor of Philosophy


School of Science

First Advisor

Associate Professor Marco Ghisalberti

Second Advisor

Professor Paul Lavery

Third Advisor

Dr Kathryn McMahon


Aquatic canopies provide important ecosystem services such as improved water quality, oxygen flux, sediment stabilisation and trapping and recycling of nutrients. The ecological health of coastal canopies and the significant ecosystem services they provide depends largely on the continuous exchange of dissolved and particulate materials across the canopy boundaries. In coastal environments, where flow is typically wavedominated, vertical mixing is believed to be the dominant process controlling residence time and, therefore, exchange. However, experiments have shown that wave-driven flows over rough boundaries, such as canopies, generate strong onshore mean currents (75% of the orbital velocity far above the canopy) near the canopy top. Since these currents can significantly influence canopy residence time, it is imperative to understand how the two processes of vertical mixing and horizontal advection can influence water renewal and, ultimately, residence time in wave-dominated canopy flows. This thesis presents predictive formulations for (i) vertical mixing and (ii) horizontal flushing, the two key mechanisms dictating water renewal and ultimately residence time in these environments. It is also examined how embedding realism (in the form of flexibility and buoyancy) in the model vegetation can influence flow and turbulent structure as well as residence time. Finally, through consideration of a Peclet number Pe (the ratio of diffusive to advective time scales), a framework for quantitative prediction of residence time in these environments is presented.

It is found that two important mechanisms dominate vertical mixing under wavedominated conditions: a shear layer that forms at the top of the canopy and wake turbulence generated by the stems. By allowing a coupled contribution of wake and shear layer mixing, a predictive formulation for the rate of vertical mixing in coastal canopies across a range of wave and canopy conditions is presented. Results also reveal that flexibility can significantly alter the hydrodynamics of the flow, shear layer characteristics and near-bed turbulent intensities. These differences ultimately lead to a significant reduction in the rate of vertical mixing in flexible canopies when compared to the rigid analogues such that vertical diffusivity in flexible vegetation was always lower than the correspond ing rigid canopy (by up to 35%). A physical description of, and predictive formulation for, the mean current generated in wave-dominated flows over large benthic roughness (such as the canopies of seagrass, macroalgae and corals) is also presented. This model indicates that the magnitude of the wave-driven current increases with the above-canopy oscillatory velocity, the vertical orbital excursion at the top of the canopy and the canopy density. An extensive laboratory study, using both rigid and (dynamically-scaled) flexible model vegetation validated the accuracy of the proposed model. Results reveal that Pe depends heavily on wave and canopy properties and may vary significantly in real coastal canopies. Quantitative predictions for residence time in the limit of Pe << 1 (mixingdominated exchange) and Pe >> 1 (advection-dominated exchange) are presented. The results of this study can have significant implications for a range of environmental, ecological and biochemical studies as well as numerical simulations. In particular, it enables an enhanced predictive capability for the residence time of ecologically-significant materials such as nutrients, seeds, pollen as well as contaminants and dredging plumes. Additionally, the greatly improved understanding in the hydrodynamics of oscillatory canopy flows achieved through this study can serve as a foundation for the numerical modelling of these environments. Ultimately, the results of this study are a step towards an improving management and protection of coastal canopies and their associated ecological communities.


Chapters 2, 3, and 4 are unavailable in this version of the thesis. See list of related publications.