This paper aims to study the composition of the phytoplankton and phytoperiphyton and some limnological aspects in the Urubuí River basin at North Peripheral Amazon, Brazil. The samples were collected during the flood and ebb periods of 2002 and 2003. Urubuí River (01°59’38”-02°37’5”S; 60°01’38”-60°01’48”W) is characterized by acidic water (pH » 4.7) with dark color, a low sediment load, and high content in dissolved organic matter derived from broken down plant material and from the production of humic substances. The river is controlled by the annual inundation of the Negro River. Temperature, pH, conductivity, oxygen, COD, potassium, total nitrogen, nitrate, nitrite, ammonium, phosphate, and silica were measured in four stations of the river. During this survey, 147 taxa were recognized and chlorophytes (49.7%) and chromophytes (28.6%) were the more abundant groups. During the ebb periods the highest richness were registered with 64.7%. Zygnemaphyceae (44%), Bacillariophyceae (26%), and Euglenophyceae (14%) were the most representative taxonomic classes. Linear regression analyzes showed that the nitrogen forms (total N, N-NO3- and N-NH4+) had large influence on the distribution and species richness.