ABSTRACT Phytoplankton is formed by photosynthesizing microorganisms that act as primary producers in distinct water bodies. These include microalgae and cyanobacteria. It is essential to know the phytoplankton in water catchment areas intended for drinking water treatment once their excessive density may result in problems, such as taste and odor in the water, toxin production, filter clogging, and other damages. This study investigated the phytoplankton dynamics and the environmental factors that may influence phytoplankton density in the drinking water catchment zone of Macapá, a city located on the Amazon River mouth. The sampling was carried out monthly from April/2015 to March/2016. The study reports the first detailed information on the phytoplankton in the study area since previously published studies regarded only cyanobacteria. The species Limnothrix planctonica and Aulacoseira granulata may substantially influence the water treatment due to their great abundance in the study area, especially in July and November, when their density peaks occur, respectively. Nevertheless, Aulacoseira granulata is the primary constituent of the phytoplankton biovolume. This study provides biological and sanitary information to guide public administration towards improving the quality and safety of water supply services, and also to increase the biodiversity knowledge of Amazonian phytoplankton.