Deepor Beel is one of the most important wetlands in the Brahmaputra Valley of lower Assam, India and is representative of the wetlands found within the Burma Monsoon Forest biogeographic region. A part (4.14 km²) of the wetland as been proposed as a wildlife sanctuary (1989) and a larger 40 km² of the wetland was declared as a Ramsar wetland of international importance (2002). Rani and Garbhanga Reserved Forests (232.3 km²) are contiguous to the wetland and they form a unique wetland-forest ecosystem. The forests house endangered Asian elephants in addition to other birds and animals. The elephants depend on the wetland for water and food. The Indian railways have constructed Assam state's southern railroad along the southern boundary (and through) Deepor Beel in 2001. That has fragmented the wetland to threat least two subsystems and also segregated the wetland-forest ecosystem. Accelerated elephant habitat degradation has been observed in the wetland after the railroad construction. Further, there are reports of elephant death due to the railroad. An attempt has been made in this study to use GIS and modeling tools to quantify the impacts of the present railroad on Deepor Beel ecosystem with special reference to elephants. The tools used in this study may used for future analyses of Deepor Beel and similar ecosystems.