During the various hydrological periods in 2011, we studied the phytoplankton along an 87-km stretch of the Araguari and Falsino rivers, which are located in the eastern Brazilian Amazon, in the state of Amapá, Brazil, the most ecologically preserved state in the country. In the study area, the aquatic ecosystem is under pressure from human activities such as, mining, hydroelectric power generation and urbanization, which contrast with the surrounding areas that are designated for biodiversity conservation. The aim of this study was to characterize the composition, frequency and richness of algae species and also to identify spatial-temporal patterns of taxa distribution. During the study period, we identified 185 taxa (136 species in 49 genera). The division Chlorophyta (class: Zygnematophyceae) presented the greatest number of taxa, whereas the division Rhodophyta accounted for only 1% of the taxa recorded. Most of the species identified (69%) were classified as sporadic in occurrence. The few taxa that were classified as common belonged mainly to the group Bacillariophyta. Species richness was greatest richness in the lentic stretches (in a reservoir) and in November (during the dry season). Of the 185 taxa identified, 174 are new records for the state of Amapá.