Climate change has become an increasing global concern, where more frequent, long lasting and severe weather extremes affect water resources around the world. Freshwater/groundwater resources in Bangladesh are one of the most important aspects of the country, which in future will be significantly affected. Global warming has been affecting the characteristics of drinking water level in many ways. The predicted changing environmental conditions suggest that we should be particularly concerned about the over use of groundwater and its withdrawal. In Bangladesh and nearby countries the effect of climate change has been studied but the nature of relationships between renewable freshwater/groundwater resources, temperature, rainfall and flood affected areas (AA) have not been examined in the manner done in this paper. This article examines the relationships between freshwater/groundwater level in terms of temperature changes, rainfall levels and flood AA during the period of 1962-2015. The quantile regressions show the three variables affect the fresh water levels with varying levels of significance (1, 5, 7 and 10% for example). This study uniquely examines the results from two modelling tools namely, STATA and EVIEWS; and confirms the similarity of the results. Freshwater/groundwater resources are negatively affected by temperature changes, rainfall levels and positively affected by flood affected area coverage -flood allows stagnant water filtration to groundwater over time. Temperature causes evaporation of stored water and rainfall causes runoff in early stages but in flood conditions the effect is positive and this is shown by the quantile regression results.