The current study was conducted to measure the activity concentration of the gross alpha and beta in 87 groundwater samples collected from the productive aquifers that constitute a major source of groundwater to evaluate the annual effective dose and the corresponding health impact on the population and to investigate the quality of groundwater in Jordan. The mean activity concentration of gross alpha and beta in groundwater ranges from 0.26 ± 0.03 to 3.58 ± 0.55 Bq L−1 and from 0.51 ± 0.07 to 3.43 ± 0.46 Bq L−1, respectively. A very strong relationship was found between gross alpha and beta activity concentrations. The annual effective dose for alpha and beta was found in the range of 0.32–2.40 mSv with a mean value of 0.89 mSv, which is nine times higher than the WHO recommended limit and one and half times higher than the national regulation limit. The mean lifetime risk was found to be 45.47 × 10−4 higher than the Jordanian estimated upper-bound lifetime risk of 25 × 10−4. The data obtained in the study would be the baseline for further epidemiological studies on health effects related to the exposure to natural radioactivity in Jordan.