Abstract: Background and Objective: Water quality in freshwater bodies is involved with multiple aspects such as physical, chemical and biological processes and their interactions. Due to the vulnerability of water resources, quality control of surface water is one of the key issues in environmental conservation programs. The objectives of the present work were to study the water quality in the Anzali Lagoon and to study the classification of water based on the water quality index in different parts of the Anzali Lagoon. Materials and Methods: In this study, we sampled water from January to December, 2015 in the Anzali Lagoon. All physicochemical parameters were sampled and determined according to standard methods. Results: The Water Quality Index results showed the Anzali Lagoon water quality had been "medium" in site 1 and "bad" in sites 2, 3 and 4. The result showed a significant difference between sit 1 and sites 2, 3 and 4 (p<0.05). However, there was no significant difference between sit 2, 3 and 4 (p>0.05). The result showed a clear spatial separation among parts in the Anzali Lagoon. The Eastern part of the Anzali Lagoon showed lower water quality compared to the central and western stations. Conclusion: This study showed that the level of pollution was different on all of the Anzali Lagoons. The water of the Anzali Lagoon has different quality classes according to the aggregation methods employed. Nutrient loadings from the adjacent agricultural lands combined with high mean salinity values affect all organism conditions. The three primary sources of nutrients, including fertilizers used in agriculture, household waste and livestock waste, reduced the water quality of the Anzali Lagoon.