Collection and analysis of environmental DNA (eDNA; genetic material that organisms shed into their environment such as sloughed cells and other wastes) enables detection of organisms without direct observation, promoting earlier detection and more rapid response than conventional sampling methods. Although eDNA analysis has been applied extensively in lentic systems, there is a limited understanding of the ecology of eDNA in lotic systems. For example, flowing water may confound the relationship between eDNA concentration and target species biomass by influencing eDNA degradation, dilution, and resuspension. I aimed to quantify the effects of downstream transport on eDNA concentration, using invasive zebra mussels (Dreissena polymorpha) in Texas reservoirs as a case study. My objectives were 1) define the rate of eDNA decline during downstream transport and 2) evaluate how abiotic factors of the river affect eDNA concentration during transit downstream. I sampled eDNA at five sites at varying distances downstream from six zebra mussel “infested” Texas reservoir and one zebra mussel “eradicated” reservoir and used quantitative PCR to measure zebra mussel eDNA concentration. I also collected environmental parameters at each site, including water temperature (°C), turbidity (NTU), and specific conductance (µS/cm). Zebra mussel eDNA concentration varied between sites of the same lake and between different lakes. Two lakes significantly decreased in zebra mussel eDNA with increasing downstream distance whereas one lake significantly increased in zebra mussel eDNA. The “eradicated” lake had positive detection of zebra mussel eDNA. I also found that none of the abiotic factors significantly affected eDNA quantity while moving downstream, contrary to the literature. Understanding the dynamics of eDNA and flowing water will further enable the ability to accurately locate the source of organisms, including invasive species, in lotic systems