Groundwater management in urban areas requires a detailed knowledge of the hydrogeological system as well as the adequate tools for predicting the amount of groundwater and water quality evolution. In that context, a key difference between urban and natural areas lies in recharge evaluation. A large number of studies have been published since the 1990s that evaluate recharge in urban areas, with no specific methodology. Most of these methods show that there are generally higher rates of recharge in urban settings than in natural settings. Methods such as mixing ratios or groundwater modeling can be used to better estimate the relative importance of different sources of recharge and may prove to be a good tool for total recharge evaluation. However, accurate evaluation of this input is difficult. The objective is to present a methodology to help overcome those difficulties, and which will allow us to quantify the variability in space and time of the recharge into aquifers in urban areas. Recharge calculations have been initially performed by defining and applying some analytical equations, and validation has been assessed based on groundwater flow and solute transport modeling. This methodology is applicable to complex systems by considering temporal variability of all water sources. This allows managers of urban groundwater to evaluate the relative contribution of different recharge sources at a city scale by considering quantity and quality factors. The methodology is applied to the assessment of recharge sources in the Barcelona city aquifers.