Abstract The aim of the present study is to determine the species composition, the structure of the fish assemblages, and to develop ecological indices in the restored east Al-Hammar Marsh. Fish were collected from October 2005 to September 2006 at two stations (Mansoury and Burkah). Fish samples contained freshwater species, both native and alien, and marine species. Thirty-one species were collected, eleven of them marine, the rest freshwater. Native species numbered 14 (45%), alien species 6 (19%) and marine species 11 (36%). Resident species formed 32.2%, seasonal species 16.0% and occasional species 51.6% of the fauna. The abundance of species varied, Liza abu being the most dominant species, with Carassius auratus ranking second and Acanthobrama marmid ranking third, comprising 35.8%, 23.6% and 10.6% respectively. Ecological indices were as follows: diversity ranged from 1.07 in November to 2.01 in July, richness ranged from 0.74 in December to 2.83 in July, and evenness ranged from 0.48 in November to 0.84 in December. The highest monthly similarity was in May at 77% and lowest in December at 29%. Water temperature showed medium correlations (0.62 and 0.58) with both the number of species and the total catch, respectively, while salinity exhibited weak positive correlations (0.05 and 0.26) with both the number and the total catch of species, respectively. Temperature is related to species number, presumably as a surrogate for many other seasonal changes.