In order to evaluate the health of the aquatic ecosystem, chemical analysis and trace elements of sediments of the Meyqan wetland in western Iran were sampled at 10 points of surface sediments (at a depth of 0–10 cm) stratified randomly and classified with five replications at each point. The samples were passed through a 63-micron sieve and placed in an oven for 24 h at 70 °C for preparation and extraction. The lowest and highest chemical properties were observed in sampling stations 3 and 6, respectively, so that the amount of TDS, Ca+2, Mg+2, Na+, Cl−, k+, SO4−2, and HCO3− in station 3 was 881.65, 4.88, 3.98, 5.62. 4.67, 0.07, 6.18, and 3.69 mg/kg, respectively, and in station 6 1100.72, 6.09, 4.96, 7.01, 5.83, 0.08, 7.71, and 4.6 mg/kg, respectively. The range of changes in the electrical conductivity (EC) of wetland sediments was from 1458.85 and 1821.34 with an average of 1558.56 μmhos/cm, which is classified as non-saline. The range of pH changes was from 7.35 to 7.94. It was found that mean concentrations of Cu (1.16 mg/kg), Ni (0.86 mg/kg, Pb (0.47 mg/kg), and Zn (0.12 mg/kg) were lower than the geochemical background values. The trace element concentrations were found in the order: Cu > Ni > Pb > Zn. The range of biotic coefficient (BC) ranged from 1.1 to 3.2 with an average of 1.74. According to AMBI, all stations except stations 1 and 3 showed slightly polluted status. Stations 1 and 3 had normal pollution classes. The average Igeo values of the trace elements trend as follows: Pb (− 5.38) > Cu (− 6.64) > Ni (− 7.1) > Zn (− 9.99). According to the Igeo classification, the values calculated for all sampling stations were less than zero, indicating that the sediments of the wetland are not polluted. The average value of Er for trace elements decreases as follows: Pb (0.19) > Cu (0.11) > Ni (0.06) > Zn (0.0017), showing a low level of contamination according to the risk index classification. The RI index was 0.35, indicating that the wetlands were not polluted. Spatial distribution maps revealed that trace elements exhibited distinct spatial patterns, with a larger concentration of Ni and Cu near the wetland’s south end. The highest concentrations of Zn and Pb were observed in the western and northeastern parts of the region, respectively. This study provides useful information on the health of the Meyqan wetland ecosystem and provides reports that can assist local authorities in selecting and developing sustainable policies to control and reduce human emissions.