Until recently, the distribution of diatom and chironomid assemblages and their attributes (species richness/diversity) in relation to water depth and sedimentary environments have been identified but not quantified. The influence of environmental variables on assemblage distribution and taxa richness in a deep, monomictic lake in Sao Miguel Island is assessed. Attention is given to community variation along a water -depth gradient. Sediment core samples were analysed for diatom content, chironomids, and grain-size clastic particles along three transects from the shoreline to the central deep basin of the lake at a resolution of 1 m water depth. Linear and unimodal regressions were used to test taxon richness, taxon diversity and taxon evenness versus water depth of each transect. A hump-shaped relationship between species richness and water depth was noted, with a peak occurring at mid-depth, meaning that samples located at that depth better represented the total subfossil assemblage living in lake Azul. Moreover,data indicate that both assemblages in Lake Azul, and taphonomic effects, were influenced by processes of clastic transport depending on the lake morphology. Results from this study allow us to access the spatial distribution of biological assemblages in clastic-dominated lakes with a high topographic gradient, and provide us with principal criteria that will allow us to determine coring locations that capture the true species diversity for studies in lakes.