Water quality status of marshes within Mesopotamia has been investigated, and temporal and spatial changes determined by examining causes and effects. Data gathered from pre-desiccation and after re-flooding periods were subjected to index and statistical analysis. The quality of waters in the region was assigned to polluted class, regarding specific salinity related parameters. Total dissolved solids, chloride and sulfate were main variables negatively impacting the water quality. The main quality parameters creating spatial differences between the selected marshes were electrical conductivity and total dissolved solids. Temporal differences in dissolved oxygen, salinity, nitrate and phosphate concentrations between the 1980's and 2000's reflected the impact of desiccation and water shortage on the marshes. Salinity and nutrient concentrations generally increased after desiccation compared to their historical levels. These findings indicated that the Mesopotamian marshes had poor water quality due to increase in the concentration of salinity. The study revealed that the index and statistical methods are useful tools identifying water quality and fingerprinting pollution. This will help decision makers to establish strategic and comprehensive water management plans.