The Biological and ecological studies of the water resources are one of the most important subject in researches and scientifically assessment. For this purpose, identifying the ecosystem, Organisms and environmental factors are the first step of this scientifically researches. Water quality assessment through permanent monitoring is the base of a program for controlling and decreasing of pollution. Biological communities are extremely sensitive to water quality and they influenced by pollutant factors. Therefore, they could be considered as an water quality’s index in water ecosystem. The use of Benthic macroinvertebrate as a bioindicator, is the most practical methods of water quality assessment. Choghakhor wetland is located in a special climate status (central Iran plateau) in Chaharmahal Bakhtiari province. This wetland was recorded as the international wetland, in the Ramsar convention and has particular importance. Despite having great socio economical and ecological importance for the local residents and ecological for birds (especially in winter). so far, no complete program regarding The health assessment and suitable management for this wetland has been done. The present investigation is focused on the use of some bioindicators, to evaluate the water quality of Choghakhor wetland. In order to estimate the qualitative indices (WQI، BMWP, HBI, ASPT), richness indexes and macroinvertabrate diversity, ten stations were chosen, as they covered whole surface of Wetland. In order to analysis of physicochemical factors and identification of benthic organisms, water and sediments sampling were done with the frequency of every 45 days, from may to march 2010. Water Quality Index (WQI) was Measured using eleven water quality parameters including Nitrate, Nitrite, Alkalinity, Hardness, Turbidity, Conductivity, Dissolved Oxygen, Ammonium, Total Dissolved Solid, pH and Biochemical Oxygen Demand. The result of WQI showed that Choghakhor water quality is not in a good condition and during the studied period the water quality was evaluated as very poor and inappropriate Keywords: Bioindicators, Diversity Indices, WQI, Benthic Macroinvertebrate, Choghakhor Wetland.