Future magnetic-confinement nuclear fusion experiments will be using neutral beam injection (NBI) systems for plasma heating that are based on sources for negative hydrogen ions as opposed to the positive ions mostly used to date. An unavoidable effect in negative NBI (NNBI) systems is the creation of positive ions in the acceleration region due to collisions between the fast negative ions and the neutral background gas. These positive ions are accelerated back into the ion source. At the high extracted ion current densities from NNBI sources and the high acceleration voltages—1 MeV in the case of ITER—the resulting heat load on the backplate of the source and the sputtering rates of the backplate material can be substantial. In this work, sputtering probes and a simple 1D calculation were employed to estimate the flux density of the backstreaming ions in the rear part of the ion source at the long pulse NNBI testbed MANITU (20 kV extraction voltage). It was found that the flux of backstreaming ions is approximately between 0.8 and 2.5% of the flux of negative ions extracted from the source. Experiment and theory are in fair agreement.