The decay of rivers and river water pollution are common problems worldwide. However, many works have been performed on decaying rivers in India, and the status of the water quality is still unknown in Jalangi River. To this end, the present study intends to examine the water quality of the Jalangi River to assess ecological status in both the spatial and seasonal dimensions. To depict the spatiality of ecological risks, 34 water samples were collected from the source to the sink of the Jalangi River with an interval of 10 km while 119 water samples were collected from a secondary source during 2012–2022 to capture the seasonal dynamics. In this work, the seasonality and spatiality of change in the river’s water quality have been explored. This study used the eutrophication index (EI), organic pollution index (OPI), and overall index of pollution (OIP) to assess the ecological risk. The results illustrated that the values of OPI range from 7.17 to 588, and the values of EI exceed the standard of 1, indicating the critical situation of the ecological status of Jalangi River. The value of OIP ranges between 2.67 and 3.91 revealing the slightly polluted condition of the river water. The study signified the ecological status of the river is in a critical situation due to elevated concentrations of biological oxygen demand, chemical oxygen demand, and low concentrations of dissolved oxygen. The present study found that stagnation of water flow in the river, primarily driven by the eastward tilting of the Bengal basin, triggered water pollution and ecological risk. Moreover, anthropogenic interventions in the form of riverbed agriculture and the discharge of untreated sewage from urban areas are playing a crucial role in deteriorating the water quality of the river. This decay needs substantial attention from the various stakeholders in a participatory manner.