The Mesopotamian marshlands faced a massive destruction from many years and this lead to effect to ecosystem. In this study a survey was made on the physical chemical and heavy metals characteristics and microbiological analysis of AL Chibaish marsh during the two months. Water analyses revealed unacceptable values for almost all physiochemical and biological properties, according to WHO standard limits for drinking water. Almost all major ions and heavy metal concentrations in water showed a distinct decreasing trend at the marsh outlet station compared to other stations. In general, major and minor ions, as well as heavy metals exhibit higher concentrations in location 1 than in location 3. The concentrations of heavy metals in water showed that all samples were contaminated by Pb, Fe, Zn, Cd and Cu. element concentration decreasing trend at the marsh outlet station compared to other stations indicate that the marsh plays an important role as a natural filtration and bioremediation system. Then format a relationship between water salinity and electrical conductivity and another relationship between turbidity. In this study many species of fungi were isolated from marsh water (WQ-1, WQ-2 and WQ-3 points) such as Trichoderma spp., Trichoderma korizanium, Aspergillus fumigates, Rhizoctina spp., Talaromyces flavus and Neosetophoma samarorum. The fungus Neosetophoma samarorum was the isolated from Iraq at the first time in this study. So the results of present study showed No growth of bacteria in all media were used.