The influence of environmental variables on planktonic biodiversity is widely known. However, the absence of information about the cyanobacterial community in tropical estuarine regions motivated this work, whose objective was to investigate the spatio-temporal variation of cyanobacterial density related to physicochemical factors in a Brazilian Amazonian estuary. For the qualitative and quantitative study of cyanobacteria and physicochemical variables, samples were collected in April/July/2009 and April/August/2010. We identified 31 species of the orders Chroococcales, Oscillatoriales and Nostocales. Species of the genera Aphanocapsa, Dolichospermum, Komvophoron, Microcystis, Pseudanabaena and Merismopedia were frequent and abundant throughout the study period. Some of the found genera have already been described as potential toxin producers. The dynamics of cyanobacteria were temporal, the highest densities occurred in 2010 (average= 1080.86 ± 702.86 cells.mL-1) mainly influenced by the high values of pH, temperature, electrical conductivity, total dissolved solids, ammonium nitrogen which led cyanobacteria to present different responses in terms of richness, density and diversity between the years.