Indian statutes identify twelve different types of biomedical wastes and give the treatment and disposal options for each. Since it is not possible for every generator of biomedical waste to go for their own treatment and disposal facility, the small-scale generators take the service of centralized treatment and disposal facilities available to them on payment. In the state of Kerala in India, where the basic health indicators match those of many developed countries, the centralized biomedical waste treatment facility is run by Indian Medical Association (IMA), Kerala, under the banner IMAGE (IMA Goes Eco-Friendly) at a place called “Kanjikode” in the Palakkad District. The facility receives biomedical waste from around 4500 hospitals across the State and an equal number of medical laboratories. The plant incinerates the incinerable waste and the other kind of waste are disinfected and decontaminated. The residual ash and dried sludge are then moved to the landfill area. Recently, the facility was in the middle of a controversy due to the alleged health hazards it posed to the surrounding population. An environmental forensic investigation was carried out at the site to establish the merits of the allegation. The reported study is a part of the investigation where groundwater was analysed for the presence of heavy metals. As the biomedical waste contain heavy metals like Zn, Pb, Cd, Cr, and Hg, the presence of these were analysed to establish contamination of groundwater by the facility. The study area is bounded by Malampuzha dam and Korayar river. Groundwater contaminant transport modelling was done for a 3430 m × 3960 m area surrounding the waste treatment facility using Visual MODFLOW and MODPATH. Ground water flow direction and particle pathlines were computed to track the movement of contaminants. Groundwater samples were collected from the area shown to be polluted by the model, if metals were discharged by the facility, and also from outside this area. Water samples were collected conforming to the guidelines in the “Pollution Crime Forensic Investigation Manual” published by INTERPOL. The collected water samples were tested for heavy metal concentration using atomic absorption spectroscopy (AAS). The water sample analysis showed that the groundwater is not contaminated by heavy metal discharge from the biomedical treatment facility.