Biodiversity intactness index (BII) was applied to monitor the deuteriation of diversity status of East Hammar marsh (EHM). Proposed bench mark list of 30 fish species existed in EHM after inundation in 2003 was initiated. Number of fish species recorded by previous authors varied between 22 to 44. In total, 35 non-native out of 52 total fish species recorded in EHM represent 67.1% of fish assemblage. Values of Shannon and wiener biodiversity index fluctuated between 1.89 & 2.9 and were positively related to an increase in salinity of EHM. As result of the increased salinity in EHM, a rise was detected in migratory marine species and an absence of freshwater native ones. Salinity fluctuation plays a major role in altering the composition of fish assemblage in EHM.The highest BII value observed at EHM was 103.57, and the lowest score was 52.07. The highest salinity value recorded was 16.1psu in EHM in August 2018. Salinity fluctuations in EHM play a major role in increasing or decreasing BII values through migration or immigration of marine fish species to or from the marsh to the Shatt al-Arab estuary. Consequently, an opposite relationship existed between BII values and marsh salinity. The fluctuation of freshwater discharge from the Shatt al-Arab River plays a major role in salinity changes in EHM. An indirect relation exists between the BII of EHM and discharge of the Shatt al-Arab River. Non-native species tend to increase diversity value accompanied with an increase in the number of marine species. Negative relation existed between BII values and non-native species ratio in EHM. Establishing baseline BII data for fish assemblages in EHM is a vital step to create an intact reference mark.