The present study carried out an evaluation of physicochemical parameters of waters from the low Tapajós river, and the identification of dominant cyanobacteria in the blooms that occurred in a transect bordering the Santarém city waterfront, in the State of Pará, Brazilian Amazon. Five (5) sampling stations were selected along the waterfront (RT-E1, RT-E2, RT-E3, RT-E4, RTE5), where water, phytoplankton and general environmental data were collected during 10 field campaigns, at intervals of 48 hours, between January 13th and 31st 2015, at the very beginning of the rainy season. The sample collections were conducted at an average depth of 2.3 meters, always early in the morning and following the procedures of the Collection and Preservation Guide and Water Samples of the Brazilian National Water Agency. Quantitative analyses of the physicochemical parameters were performed, namely: hydrogenionic potential (pH); water temperature (ºC); turbidity (NTU); electrical conductivity (EC); Dissolved Oxygen (DO); nitrate (NO-3); nitrite (NO-2); ammonium ion (NH4); ammonia (NH3); orthophosphate (PO43-); phosphate (P2O5); phosphorus (P); iron (Fe) and chlorophyll a (Chlo a). General descriptive statistics were calculated. For counting of individuals, the efficiency was superior to 80%, reaching a total of 3,910 individuals, from which 38% are species of the Cyanophyta division. The following species were dominant: Synechocystis aquatilis Microcystis aeruginosa, Dolichospermum spiroides, Nostoc sp. Except for S. aquatilis, all the others are cyanotoxin producers that can be released into the water after cell disruption. The presence of cyanobacteria potentially producing cyanotoxins is of concern and should be considered in the diagnosis of waterborne diseases, such as hepatic infections that affect the riverine population of the Tapajós river.