Diatoms are powerful bioindicators, as each species has a specific tolerance for environmental variables, they are abundant in aquatic ecosystems and they respond rapidly to change. The use of diatoms as bioindicators is widespread especially in streams, rivers and natural lakes and is increasing in reservoirs. Typically, diatoms utilised in streams and rivers for biomonitoring consist of living benthic communities attached to rocks, while in lakes and reservoirs diatoms collected from the sediments consist of senescent planktonic diatom that have settled out of the water column. The development of diatoms as indicators in reservoirs can be problematic due to the complex hydrology and higher rates of sedimentation associated with these systems. Despite these challenges the use of diatoms in reservoir environments to develop transfer functions to infer historical changes in water quality is increasing. The development of regional datasets is important, as using indicators or transfer functions that have been developed in other areas to quantify changes in water quality does not provide accurate results.The aim of this thesis was to develop diatoms as bioindicators of water quality in freshwater reservoirs of subtropical south east Queensland (SEQ), to complement the traditional water quality monitoring across different sites. This will provide understanding of environmental drivers of diatom assemblages in this region. The diatom assemblages of reservoirs in this region have not been investigated to date and this study will provide the first investigation into their biological diversity and the water quality histories of the reservoirs.This study was undertaken in drinking water reservoirs of subtropical south east Queensland, Australia. Spatial variability of the sediment surface diatom assemblage was investigated in the Lake Wivenhoe, the largest reservoir of the region which supplies over two million people with drinking water. The diatom assemblage of surface sediments was found to vary spatially within a reservoir and aligned with zonation that is typical of reservoir environment, lacustrine, transition and riverine. Three groups of diatoms characterised the reservoir, taxa reported as cosmopolitan were found throughout, higher abundances of planktonic taxa were observed in the lacustrine zone and benthic taxa were reported in the riverine zone. i Sediment samples were collected from 15 reservoirs in south east Queensland. The diatom assemblage and corresponding water quality parameters from each site were used to develop transfer functions specific for the region. Robust models were developed using weighted averaging partial least squares for conductivity and total phosphorus. The optimum and tolerances of these parameters are reported for 116 diatom taxa.Early in 2011, the largest rainfall on record took place in the Wivenhoe dam catchment which resulted in an extreme inflow into the reservoir. One core had been taken in October 2010 to determine historic changes in the diatom assemblage. Following...