The present study evaluates the vulnerability of the lake system (Deepor Beel) due to the combined exposure of toxic metals, major ions and mineral dissociation. The hydro-chemistry of the Deepor Beel lake reveals the dominance of carbonate weathering with strong evidences of ion-exchange reaction occurring throughout the monsoon season of 2014 and 2015. Through an integrated application of multivariate analysis, the occurrence of albite weathering was confirmed, although as an isolated incidence only, along-with substantial evidence of waste water intrusion from fertilizer industries. The moderate cation exchange capacity (CEC) of the soil, indicates the presence of illite, chlorite and kaolinite which provides a strong buffering action in terms of phosphorous and nutrient retention. However, occurrences of chemical waste in the form of bleaching powder (Ca(OCl)2) are causing acidification of lake soil, which will trigger the release of phosphorous and may enhance the eutrophication level in near future. Through the simulations of Biotic Ligand (BL) model on ceriodaphnia dubia, it is being revealed, that the free availability of Ca2+ in the lake water, provides a higher adsorptive competition for labile metal species especially for Cu and Zn. Additionally, the risk among children from drinking lake water, has increased by three to seven times in a duration of just one year. The present study is a pioneering work, which has evaluated the vulnerability of Deepor Beel lake by adopting a sequential assessment strategy of lake internal as well as external ecology. Our proposed methodology can be a used as a scientific basis for future assessment of the lake health.