This research was conducted to assess the Bahmanshir river health and biodiversity using Nygard-Palmer index. Phytoplankton sampling was performed monthly by the use of a 30-micrometer mesh size plankton net at 6 different stations along the river since September 2013 to August 2014. A total of 109 species of microalgae (phytoplankton) were identified in which Bacillariophyta was the dominant phylum with 87 species. More than 90% of all samples were consisted of diatoms during the whole year excluding July and August. The phylum Cyanophyta was formed 19 and 37% of all samples in July and August, respectively. Among the species of Bacillariophyta, Coscinodiscus sp. and Coscinodiscus oculus were dominant in all months especially at the stations in marine environment of the river estury (station 5 and 6). In the phylum Cyanophyta, Oscillatoria sp. was the dominant species at station 1 and 2 (freshwater condition) in July and August 2014. The presence of pollution-tolerant algae such as Oscillatoria, Navicula, Scenedesmus, Nitzschia, Fragilaria, Pediastrum, Cymbella, Synedra, Gomphonema, Cyclotella, Pinnularia and Spirogyra at various stations of the Bahmanshir River indicated organic pollution of the river with large quantities of organic compounds. Evaluating the saprobic indices showed that all  stations excluding station 6 were in the alpha mesosaprobic class. Similar results were obtained from the Nygard-Palmer indices. The presence of pollution-tolerant phytoplanctons could be a warning sign of declining water quality in the river.