The present study was implemented in the Zachery Marsh as part of the middle marshes north of Bashar Province from January to December 2022 to investigate the impact of the seasons’ oscillation between drought and flooding on fish assemblage abundance, size spectrum, and ecological indices. Three stations were selected to collect samples of fish. The specimens were monthly gathered with different fishing tools, including fixed gillnets, cast nets, and electrofishing. The water temperature ranged from 12.32 to 34.03 °C, the salinity varied from 1.75 PSU to 2.89 PSU, and the pH fluctuated between 7.47 and 8.43. The rate of change in water depth in the low flat regions fluctuated from 27 cm in September to 76 cm in April. The mean water depth in rivers, small pits, and canals varied from 45 cm in October to the highest, 121 cm in March. In the seasonal regions, the average depth ranged from zero in July, August, September, and October to 40 cm in April. The current study documented 18 fish species belonging to 16 genera and 9 families from Zachery Marsh, all of them affiliated with the Osteichthyes class. Cyprinidae was the most abundant family, including six species. The species Planiliza abu, the most abundant species, formed 28.44%, Carassius gibelio constituted 20.27%, and Orechromis aureus represented 18.52%. The dominance index (D3) of the three dominant species was 67.23%. The size spectrum of the most commercial species was determined. The diversity index value ranged from 1.64 in August to 2.08 in June, the evenness index varied between 0.69 in May and 0.91 in December, and the richness index values fluctuated from 1.47 in August to 2.28 in June. Resident species represented 88.02%, seasonal species formed 6.08%, and the occasional fish species counted for 5.90%. The present study concludes that the fluctuation between drought and flooding has a critical role in the composition of fish assemblages, particularly in seasonal marshes that are subjected to extreme conditions. The fish evolve several reproductive strategies in these difficult conditions in order to survive and continue.