Miniaturized atmospheric pressure glow discharges (APGDs) were generated in contact with small sized flowing liquid cathode systems. As anodes a solid pin electrode or a miniature flow Ar microjet were applied. Both discharge systems were operated in the open to air atmosphere. Hydrogen peroxide (H2O2) as well as ammonium (NH4+), nitrate (NO3−), and nitrite (NO2−) ions were quantified in solutions treated by studied discharge systems. Additionally, an increase in the acidification of these solutions was noted in each case. Emission spectra of the near cathode zone of both systems were measured in order to elucidate mechanisms that lead to the formation of active species in gas and liquid phases of the discharge. Additionally, the concentration of active species in the liquid phase (H2O2, NH4+, NO3− and NO2−) was monitored as a function of the solution uptake rate and the flow rate of Ar. The suitability of investigated discharge systems in the water treatment was tested on artificial wastewaters containing an organic dye (methyl red), hardly removable by classical methods non-ionic surfactants (light Triton x-45 and heavy Triton x-405) and very toxic Cr(VI) ions. Preliminary results presented here indicate that both investigated flow-through APGD systems may successfully be applied for the efficient and fast on-line continuous flow chemical degradation of toxic and hazardous organic and inorganic species in wastewater solutions.