Islamabad is essentially the only well-planned city in Pakistan, but groundwater depletion has become a serious issue there because of the rapid increase in population, poor water management, and deforestation. The current water demand of the city is about 220 million gallons per day, with the Capital Development Authority (CDA) providing up to 70 million gallons per day. The need for water is mostly fulfilled through groundwater sources, such as water bores and commercial tube wells. Hence, identifying recharge sites for natural aquifers is a significant component of groundwater required to overcome the water crisis. Therefore, this study aims to identify potential sites for natural aquifer recharge by using analytical hierarchy process (AHP), weighted linear combination (WLC), and fuzzy logic methods. To achieve the stated objective, seven local influencing factors including soil, slope, water table, population density, land use land cover (LULC), drainage density, and elevation have been utilized in this study. AHP was utilized for the evaluation of the relative importance of the above-mentioned factors, while fuzzy logic was applied for the standardization of these factors. Finally, the AHP-WLC and fuzzy logic approaches were used to merge factor maps in order to identify suitable sites for natural aquifer recharge in Islamabad City. Two different suitability maps were constructed from both techniques, and on each of the resulting maps, the subregions were categorized into five classes: not suitable, less suitable, moderate, suitable, and most suitable. Based on the AHP-WLC results, 5% of the whole study area is deemed most suitable for natural aquifer recharge (NAR), whereas from the fuzzy logic results, 10% of the study area is marked as most suitable. In contrast, 37% and 32% of the whole study area were identified as suitable by the AHP-WLC and fuzzy logic methods, respectively. While both techniques can obtain satisfactory outcomes, the suitability map from fuzzy logic has produced more precise results. Hence, we propose to CDA-Islamabad here different sites for recharge wells based on the results of fuzzy logic. As recommended by this study, to date CDA has constructed twelve recharge wells.