Stormwater is considered as an alternative water source for both potable and non-potable uses. However, stormwater has not been widely used as an alternative water source, most likely due to a lack of knowledge about the presence and risks associated with pathogens and antibiotic resistance genes present in raw and treated stormwater and how these populations change with environmental conditions. In my thesis research, five different stormwater reuse systems (SRS) in the Twin Cities metro area were sampled from every three weeks from June to October 2019 to build a comprehensive data set for analysis of temporal dynamics of pathogens and antibiotic resistance genes (ARG) in raw and treated stormwater samples. As a follow up, two sites were time intensively sampled (i.e., sampled every 20-40 min) twice in summer 2020, along with city water and lake water control sites. Microfluidic qPCR, a high-throughput quantification tool provided microbial data for 23 bacterial pathogens, 11 viral pathogens and 48 ARGs along with physiochemical testing such as turbidity, free and total chlorine, and water temperature to evaluate environmental conditions. Correlations between pathogen and ARG levels and environmental parameters such as temperature and precipitation assess the impact of precipitation and other environmental variables on pathogen and ARG concentrations in stormwater both over the season (2019 research) and during an average run of a SRS (2020 research.) Viral and bacterial pathogens were sporadically detected both years while ARGs were widely detected. Environmental variables loosely correlated along known patterns but did not account for the variation seen in the data. The system with UV treatment and the system with a ball and bag filter sufficiently eliminated E. coli and limited the concentrations of ARG/pathogen genes, whereas the chlorinated system did not. These results will be helpful when designing stormwater reuse systems in the future.