Innovative technologies are needed to enhance access to clean water and avoid waterborne diseases. We investigated the performance of cold atmospheric plasma (CAP), a clean and sustainable approach for microbial inactivation and total organic carbon (TOC) degradation in environmental water. Water matrices played a crucial role in the performance of CAP efficacy; for example, complete removal of ɸX174 from dH2O required 1 min of treatment, while ɸX174 reductions of ~ 2log10 and 4log10 were obtained after 10 min of CAP exposure in river water and wastewater samples, respectively. Similarly, after 10 min of CAP treatment, bacterial concentrations decreased by 3 log10 and 4 log10, in river and wastewater samples, respectively. In contrast, after 30 s of contact time, a 4 log10 reduction of bacteria was accomplished in dH2O. Complete removal of Acanthamoeba from dH2O was found after 30 min of CAP treatment, whereas it was not removed from surface water or wastewater at the same exposure time. Additionally, the approach successfully reduced TOC, and the degradation kinetics of TOC were represented by pseudo-first-order. CAP showed higher rates of TOC degradation in the final effluent of the wastewater treatment plant compared to surface water. The difference in CAP performance between river water and wastewater could be attributed to the bulk structure of humic acids in river water compared to small organic byproducts in the final effluent of WWTP. Overall, the findings reported here support the idea that CAP holds promise as a sustainable solution for controlling pathogens, removing organic water pollution, and integrating with traditional purification processes. Low-cost systems may advance CAP technology and increase its widespread use.