The reliable estimation of groundwater recharge is fundamental to the appropriate use of groundwater resources. Shallow groundwater resource quantification for irrigation in highland regions remains challenging. Specifically, in the humid Ethiopian highlands, only limited research has been done on groundwater recharge estimation. Despite the various techniques used to determine recharge, the objective of this study was to better understand natural groundwater recharge using water table fluctuation (WTF) and empirical methods in the sub-humid Ethiopian highlands. The Ene-Chilala watershed was selected for this study. Precipitation, infiltration rate, and piezometric water levels were measured. Precipitation was measured over a 4-year period (2013–2016), whereas infiltration and the groundwater table were measured over a 1-year period (2014). Recharge rates using WTF were determined from the three slope positions and the median of all piezometers for the whole watershed. Infiltration rates on the upslope were greater compared to the mid- and downslopes. The rainfall intensity exceeded the infiltration rate in all slope positions, so the excess rainfall recharged the perched upslope aquifer and eventually drained as interflow to recharge the mid- and downslopes. The estimated groundwater recharge from WTF was less compared to the average of empirical estimations. Surprisingly, from the nine selected empirical equations, the modified Chaturvedi formula had a similar estimation to the WTF method. In conclusion, it is challenging to find long-term seasonal and spatial groundwater-level data. Long-term groundwater data should, therefore, be available in order to arrive at a reliable recharge estimate and for effective groundwater management practices.