Chalan beel, the largest natural depression in Bangladesh is under threat due to population pressure, over exploitation, change of water courses, pollution and siltation. Therefore, a study was conducted to assess the habitat and biodiversity status in dry and wet seasons through MODIS AQUA 250 m images and Geographical Information Systems supported by field data from July 2010 to June 2012. The MODIS data of 2002 and 2008 were collected and analyzed to perceive the water availability, extend of water area and variety of fishes found round the year. The False Colour Composite images of blue, near infra-red and mid infra-red bands and Normalized Difference Vegetation Index of 2002 and 2008 were prepared to perform the land use and land cover changes. The data interpretation showed the trend of water receding tendency from wet to dry season in 2002 and 2008 images respectively. The occurrence of moderate and high vegetation was comparatively higher in 2002 images than in 2008. Moreover, very small water area was observed in March and April in both year images due to over use of surface and underground water for irrigation that is the threat to the natural resources in the region. Hence, steps need to be taken by the Government and stakeholders to stop fishing via dewatering and maintain the minimum water level in the Chalan beel for safe guard the aquatic biodiversity.