The organic pollution index (OPI) was applied to assess the state of the organic pollution in the southern part of Eastern Hammar marsh, Al-Chebiyesh marsh, and the Euphrates and explain the role of submerged aquatic plants in reducing the level of water pollution. Water samples were collected monthly from two stations for each part (i.e., with and without submerged plants). The OPI depended on three parameters, namely, NO3, PO4, and BOD5. Results show that the highest NO3 was 6.4 mg/L in February in Al Burka, whereas the lowest value was 2.3 mg/L in August in the Euphrates station, which contains submerged plants. The highest PO4 was 0.76 mg/L in February in Al Burka, whereas the lowest value was 0.24 mg/L in August in Saleh River’s station, which contains submerged plants. The highest BOD5 was 3.63 mg/L in August in the Al Burka station, whereas the lowest value was 0.91 mg/L in February in the Euphrates station, which contains submerged plants. The index values indicate the presence of organic pollution in all stations, with discounts varying between (65.9 and 36.2), (49.9 and 35), and (40.1 and 22) in Eastern Hammar, Al-Chebiyesh, and the Euphrates, respectively. The vital role of submerged plants in the consumption of nutrients reduced the OPI annual values to (44.4, 37.8, and 25.3) compared with the values in stations without plants (54.9, 44.6, 36). The annual values varied between the Deteriorated category in the East Hammar marsh, a Poor category in Al-Chebiyesh, and the Medium category in the Euphrates, with yearly values of 49.7, 41.2, and 30.7, respectively.