The Mesopotamian marshlands are one of the most internationally important wetlands in the Middle East as it constitutes a nursing ground for many species of birds migrating from North Europe as well as for its rich biodiversity. These marshlands have undergone significant environmental changes during the last three decades owing to decreasing freshwater discharge which has led to water quality deterioration and a changing hydrological regime. This has had a considerable effect on the fauna and flora of the marshes, diminishing their ecological value and significance. The work presented here is the first attempt to investigate the marshes environmental condition during the past two centuries using paleolimnology, specifically diatoms as bioindicators in a sediment core. 80 species of diatom belonging to 35 genera were identified. The taxa encountered in the core are a mixture of fresh and brackish water forms. These are epiphytic and benthic taxa, no planktonic species were found. The fossil diatom community shows that the marshes have been exposed to different periods of salinization as well as eutrophication. The dominance of pollution tolerant species in the core indicates poor water quality for the past 160 years. Paleolimnology is important to understand past environmental conditions and forms a milestone for successful future restoration process. Further work is required to extend the time scale to identify natural ecological states and thresholds to guide international aid restoration projects.