Macrobenthos and macrophytes of the north shore littoral zone of Hamilton Harbour were extensively sampled in late August 1994. Benthic community structure is described, including the presence of several oligochaete and chironomid genera previously unreported in the harbour. Community structure is scale dependent and identifying which spatial scales contribute important structure is a useful step in determining which environmental factors have the greatest impact on the benthic community. This information can be used to plan efficient benthos monitoring programs, and to construct spatially explicit models of the harbour ecosystem. Most of the variation in the data set (approx. 88%) is due to small scale patchiness, probably related to patchiness of the macrophyte community and sediment grain size, as well as biotic processes such as predation and competition. Large scale structure is related to a water depth gradient, probably involving changes in dissolved oxygen concentrations, light attenuation, and sediment grain size. Macrophytes also respond to this gradient. There is little important structuring of the benthos community at intermediate spatial scales. Models of benthic communities in the harbour must deal with spatial pattern effects such as autocorrelation. Additionally, spatial patterns provide information useful for understanding causes of community structure. A method is developed for the spatial pattern analysis of the benthic community data, which allows the simultaneous evaluation of patterns at various scales, with minimal mixing of information between scales. / Thesis / Master of Science (MS)