The structure and distribution of the Paraguay River phytoplankton (between 16degrees 03' and 26degrees 53' S and between 57degrees 13' and 58degrees 23' W was studied during June-July/95 and December/95-January/96. Phytoplankton density values were lower in winter (mean value between 731 and 878 ind. ml(-1)) in summer (between 1113 and 1876 ind. ml(-1)), and mean biomass (biovolume) ranged between 0.215 and 0.372 mm(3) l(-1) and between 0.586 and 1.223 mm(3) respectively. In all, 332 algal taxa were identified: 298 in the upper section (Pantanal) and 143 in the middle and lower sections. They pertained to the Cyanophyta, Chlorophyta, Euglenophyta, Cryptophyta, Pyrrhophyta, Bacillariophyceae, Chrysophyceae and Xanthophyceae. Small Chlorophyta (Chloromonas gracilis, Choricystis minor, Crucigenia quadrata, Scenedesmus ecornis, Monoraphidium contortum and M. minutum) and Cryptophyta (Cryptomonas marssonii, C. ovata and Rhodomonas minuta) dominated. Bacillariophyceae (genera Aulacoseira and Cyclotella) increased in the lower section of the river. Biomass was dominated by centric forms of the genus Aulacoseira (A. granulata and its morphotypes, and A. herzogii). The diversity index varied between 1.99 and 5.0 bits ind.(-1) in winter and between 1.49 and 4.87 bits ind.(-1) in summer. Species richness (between 4 and 105 taxa per sample) showed a decrease in north-south direction. The presence of one of the largest wetlands of the world may explain the high algal diversity in the upper section. The Bermejo River, with highly mineralized waters and a high content of suspended solids, causes a strong discontinuity in the lower section of the main course, viz, a decrease in water transparency and in the density, biomass, diversity and species richness values of phytoplankton, before its waters meet the Parana River.