Modeling of wetlands and lakes pollution is necessary for development and land allocation, management, water quality monitoring, prevention of pollution and conservation of biodiversity. In this study, physico-chemical parameters of EC, TDS, DO, pH, NO3-, PO43-, SD, TP, TN, and Chl.a, pollution and biological indices of TSI & BMWP and organic matters (OM) were used for assessment of pollution and anthropogenic impact on water quality in Choghakhor wetland in Chaharmahal Bakhtiari province, Iran. Sampling stations were selected on systematic non-random base for the sampling and measurement. Sampling was performed of wetland surface and in depth of 50 centimeter from 12 stations 1 kilometer in distance in six stages and in 45 day intervals. Then the spatial model of surface and depth average of qualitative parameters, soil organic matters, and TSI and BMWP indices was prepared using interpolation functions based on cross validation technique (lowest value of RMSE, highest value of R2 and lowest close to zero values of spatial data MBE and MAE) of deterministic and geostatistical methods in GIS environment. The results of spatial-temporal modeling for the period of 2003 to 2005 showed that values of TSI, BMWP, and OM indices with moderate values of 61, 31 and 40% are in eutrophy and bad status and the values are higher (more pollution) in south and west half of wetland due to land use activities. Also TSI, PO43- and DOsat parameters have meaningful temporal correlations and BMWP, OM, TDS and Depth parameters has significant spatial correlations. Also results of spatial-temporal modeling of TSI (2005-2006) determined the highest pollution in spring and autumn seasons (eutrophic moderate of 67-70) which is hypertrophy of 70-74 in south half due to anthropogenic and land use impact. The value is lowest in summer season showing the lower pollution with eutrophic moderate of 59.