We investigate the use of a DC-pulse-driven non-thermal atmospheric-pressure He plasma jet in the regulation of hydrogen peroxide (H2O2), nitrite (NO2−), nitrate (NO3−), and oxygen (O2) in deionized (DI) water. The production of these molecules is measured by in situ UV absorption spectroscopy of the plasma-activated water (PAW). Variations in the pulse polarity and pulse width have a significant influence on the resultant PAW chemistry. However, the trends in the concentrations of H2O2, NO2−, NO3−, and O2 are variable, pointing to the possibility that changes in the pulse polarity and pulse width might influence other plasma variables that also impact on the PAW chemistry. Overall, the results presented in this study highlight the possibility of using DC-pulse-driven plasma jets to tailor the chemistry of PAW, which opens new opportunities for the future development of optimal PAW formulations across diverse applications ranging from agriculture to medicine.