Groundwater is considered the most important natural resource to mankind. Groundwater constitutes an important part of the hydrological cycle and is more prone to pollution. Dumpsite located in close proximity to groundwater resources is highly susceptible to leachates pollution. Predicting the susceptibility of groundwater pollution is crucial to address industry-standard codes for groundwater flow, contaminant transport, local to regional-scale water quality, and source water protection issues. Therefore, predicting heavy metal transport in groundwater around Lemna dumpsite in Cross River State, Nigeria, was examined. Soil samples were purposively collected with a soil Auger, along a straight line at (5 m, 25 m and 50 m) in the dumpsite. Water samples were purposively collected from five (5) boreholes close to Lemna dumpsite. The study utilized pumping test method to obtain data for the analysis of heavy metal transport in groundwater. Data analysis of the laboratory results of soil and borehole water quality focuses on arsenic, lead, cadmium, chromium, nickel, and mercury. Paired sample t test was used to analyse the soil and borehole water quality. Visual Modflow was also used to analyse the solute transport of heavy metals in groundwater around Lemna dumpsite. The paired sample t test of the analysis of heavy metals in soil exhibited a significant difference (p < 0.05) compared to National Environmental Standard Regulation and Enforcement Agency limits. The paired sample t test of the analysis of heavy metals in borehole water exhibited a significant difference (p < 0.05) compared to World Health Organization limits. The significant level indicates contamination of the soil and borehole water. The findings revealed a spatial spread of 259.2000 m2/day, with the contaminant travelling up to 94,608 m2/year. The extent of heavy metals concentration exhibited a maximum of 0.991 mg/l to a minimum of (− 6.72 × 10–18 mg/l), with concentrations decreasing as the plume extend. The study recommends the need for remediation and stringent monitoring to mitigate heavy metal contamination of boreholes near Lemna dumpsite.