Environmental agency consultations and project siting and design by Transportation state agencies require rapid, reliable, and cost-effective methods to detect and monitor potential project constraints, such as rare, threatened and endangered (RTE) species. Sampling the environment for environmental DNA (eDNA) has proven to be an accurate and sensitive technological method for biomonitoring. As compared with conventional field surveys, sampling for eDNA is rapid, less labor-intensive, and provides an objective way to confirm species presence or absence. It also provides distinct advantages with respect to worker safety, lower sampling costs and less invasive for species and its environment. We will review the results of eDNA sampling from several Stantec projects to demonstrate the benefits of eDNA to confirm the presence of a diverse suite of aquatic species including RTE fish and invasive aquatic species, such as plants and mussels, while adjusting the sampling design to increase the probability of detection. We will also review examples of how state Department of Transportation agencies have implemented eDNA sampling in aquatic monitoring projects to augment conventional methodologies during Endangered Species Act consultations for construction monitoring and determining site specific time of year restrictions, which can have significant negative logistical and financial impacts for bridge projects in the Northeast. The Massachusetts Department of Transportation used new technologies (eDNA, acoustics, and side scan sonar) to determine the spatial and temporal distribution of endangered shortnose sturgeon (Acipenser brevirostrum) in the Merrimack River. eDNA and side scan sonar helped developed less restrictive time of year restrictions and more accurate population estimates with less impact to the endangered sturgeon.