In 2018, water flow was restored to 22 desiccated streams in East Maui, Hawaii, after over a century of diversion to support large-scale sugarcane farming in Maui's central valley and along the island’s north shore. This restoration reconnected aquatic habitats, but little research has been done to assess water quality and recovery in these restored streams. To analyze the correlation between bacterial communities and water quality variables, water samples were collected from 15 stream sites, filtered for environmental DNA (eDNA), and physicochemical and hydrological parameters were measured, including temperature, pH, dissolved oxygen, specific conductance, nitrate, ammonium, phosphate, phycocyanin, and chlorophyll a. Nutrient content was analyzed using inductively coupled plasma optical emission spectrometry (ICP-OES) and flow injection analysis. Sequencing and bioinformatics of filters containing eDNA were performed by Jonah Ventures Laboratory. Bray-Curtis dissimilarity was used to assess community variation from eDNA sequence data. A Constrained Analysis of Principal Coordinates (CAP), combined with stepwise model selection and permutation-based ANOVA, identified soluble reactive phosphorus (p = 0.019) and water temperature (p = 0.027) as significant predictors of bacterial community structure, explaining 27.6% of the observed variation. Indicator taxa such as Hydrogenophaga, Pajaroellobacter, and Tolumonas were strongly associated with high-phosphorus environments. These results support the role of nutrient inputs and thermal conditions in shaping microbial assemblages in freshwater systems. Spatial graphics illustrate these correlations to show the health of the streams on an island-wide scale. These findings and deeper analysis of pollutants and bacterial communities will guide local leaders in their restoration efforts to ensure these aquatic systems receive the resources needed to achieve water quality status that can support stable native communities.