We found by molecular dynamics simulations that a low energy ion can be trapped effectively in a nanoscale Paul trap in both vacuum and aqueous environment when appropriate AC/DC electric fields are applied to the system. Using the negatively charged chlorine ion as an example, we show that the trapped ion oscillates around the center of the nanotrap with the amplitude dependent on the parameters of the system and applied voltages. Successful trapping of the ion within nanoseconds requires electric bias of GHz frequency, in the range of hundreds of mV. The oscillations are damped in the aqueous environment, but polarization of water molecules requires application of higher voltage biases to reach improved stability of the trapping. Application of a supplemental DC driving field along the trap axis can effectively drive the ion off the trap center and out of the trap, opening a possibility of studying DNA and other charged molecules using embedded probes while achieving a full control of their translocation and localization in the trap.