The Nila river basin of Kerala state with its two important tributaries, the Kalpathypuzha and Kunthipuzha, was surveyed (from 2005 January to 2007 December) for a comparative study of the avifauna selecting three study sites each in each basin. A total of 208 species of birds was recorded from the three basins. Of the 140 species recorded from the Nila basin, 70% were residents, 29% migrants and the rest local migrants. A good number of shore birds (25species) were the major constituent of the migrants. The majority of the shorebirds were seen at Manchady, the site close to the Ponnani coast. Three species recorded along the Nila, the Darter (Anhinga melanogaster), the Black-bellied tern (Sterna auticauda) and the Asian open-bill stork (Anastomus oscitans) are threatened species. In the Kalpathypuzha basin, of the total 157 species, 87% were residents and 10.82% migrants. Of these 49 species were forest birds. The two study sites in this basin, the Kava and Manthakkad, are adjacent to forests and hence the higher number of forest birds. Of the 188 species recorded from the Kunthypuzha basin, the resident- migrant ratio is 76.31:21.68. The number of forest birds is the highest here (55species) and the majority of these were seen at Pathrakkadavu site an extension of the Silent valley forests.