Traditional invertebrate biomonitoring has low taxonomic resolution, low accuracy, and is plagued with human error and biases. Molecular monitoring, using environmental DNA (eDNA), is a practical alternative due to the high accuracy, lack of human error influencing results, and the potential for standardizing techniques across systems. This study evaluates molecular monitoring by using accumulation curves from temporally distributed samples across an impervious cover gradient, comparing traditional samples processed by Charlotte-Mecklenburg Storm Water Services to molecular samples, and eDNA sampling to quantify invertebrate communities across uncommonly monitored freshwater systems including beaver ponds, beaver wetlands, restored streams, and tribally protected Catawba Nation Reservation streams. Molecular monitoring of sites resulted in a total of 14 phyla compared to 3 phyla from traditional monitoring. Traditional versus molecular communities were significantly different (PERMANOVA, df = 1, p = 0.001). Molecular samples had greater dissimilarity in community structure compared to traditional samples. Distribution of samples based on percent impervious cover were similar across traditional and molecular samples, implying differences between sampling types does not misconstrue community structure. Lastly, multi-site type analysis revealed invertebrate community structure differences among beaver ponds, restored streams, and Catawba Nation streams at the order (PERMANOVA, df =3, p = 0.042) and family (PERMANOVA, df = 3, p = 0.043) levels. The results of this study are an indicator that molecular biomonitoring using eDNA for invertebrate communities is a successful, and more efficient, alternative to traditional biomonitoring.