This study was carried out to assess the quality of borehole water in some Local Government Areas affected by Boko Haram insurgency. Madagali and Michika were two affected Local Government Areas in Adamawa state. It was carried out in both rainy and dry seasons. Physicochemical parameters and heavy metal level contaminations were used to assess the level of pollution. Physicochemical parameters that gave critical values of Pollution Index were temperature, Dissolved Oxygen and Chloride. While the heavy metals studied were Cd, Mn, Fe, Cu and Zn. High concentrations of Cd, Fe and Mn were recorded at some sites at levels beyond the recommended values by WHO and SON. Higher concentrations of these metals were recorded during the rainy season. The Contamination Factor (CF), Contamination Degree (CD) and Pollution Load Index (PLI) were found to be low, signifying a safe level, though these metals can bio-accumulate or bio-magnify and cause health hazards. The activities of Boko Haram had greater effects on the water through the higher temperature, DO and Chloride concentrations. This could be due to explosive products that have the tendency of distorting the atmospheric conditions which invariably affected the analyzed parameters in the borehole water.