In lowland, shallow lakes, benthic diatom assemblages are affected by several parameters, including nutrient concentration, seasonality, light, and substrate. This thesis aims to establish which factors most affect these assemblages and explores the feasibility of using these organisms to monitor standing water quality. A one-year field study was carried out in five shallow lakes of varying trophic status in Norfolk, UK, in which a set of substrata (submerged, emergent and floating plants, and lake sediment) were collected for diatom harvesting. A range of physical and chemical parameters of the water column were measured on each sampling occasion. These data were subjected to multivariate analyses (PCA, DCA, RDA, variance partitioning). Diatom optima and tolerances for certain parameters were calculated and biodiversity indices were used to assess differences between diatom communities over substrates and time. Based on patterns observed in the one-year study, namely that some differentiation in diatom community composition was evident between plant species, two sets of experiments were carried out in situ. The first involved plastic plants placed into three of the lakes to assess diatom community differentiation according to plant morphology. One set was a control, whilst the other was placed into a mesh cage to reduce grazing by invertebrates. Higher numbers of diatom species were observed on the grazed plants, and vertical colonisation differences were evident. The highly divided leaved plants appeared to develop a community similar to that of the less divided leaved plants. The second experiment involved bamboo canes placed into reed beds at two sites to assess community changes along a light gradient. Actual Phragmites stems were also sampled to measure the differences between the artificial substrate and the natural ones. The epiphytic community appeared to respond to changes in light intensity and the canes developed a flora similar to that of the real stems. The factors most affecting the benthic diatom communities were substrate, and to a lesser extent, total phosphorus and light. Submerged plants are recommended as the optimal substrate for monitoring as they combine practicality with sensitivity.