Until recently, the distribution of diatom and chironomid species assemblages and their attributes (e.g. species richness and 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, monomitic lake in São Miguel Island is assessed. Attention is given to community variation along a depth gradient. Surface-sediment diatom and chironomid assemblages were collected along three transects from shoreline to the centre 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 transept. A hump-shaped relationship between species richness and water depth was noted, with a peak occurring at mid depth levels, meaning that samples located at that depth better represented the total subfossil assemblage of lake Azul. Also, diatom and chironomid assemblages in Lake Azul, and taphomomic effects, were influenced by sedimentary environmental processes depending on the lake morphology. Based on the present results, in order to determine ideal coring locations for lake studies combining diatom and chironomid analyses, an understanding of the spatial distribution of these biota is essential.