The Winooski River Basin has a long history of eutrophication and associated ecological risk. This study evaluated nutrient dynamics, trophic state, and ecological risk across lakes, ponds, and reservoirs using water quality indicators and statistical analyses. Nutrient-related Risk Quotients (RQs) were used to assess the extent to which observed conditions exceeded ecological thresholds, allowing comparison of phosphorus, nitrogen, chlorophyll-a, and worst-case risk across waterbodies. Results indicated that phosphorus is the primary driver of algal biomass, supported by a strong relationship between total phosphorus (TP) and chlorophyll-a (Chl-a), as well as consistent patterns across Carlson Trophic State Index metrics. Trophic conditions ranged from oligotrophic to eutrophic, with most sites classified as oligotrophic to mesotrophic. Principal Component Analysis (PCA) identified a dominant eutrophication gradient defined by TP, Chl-a, and water clarity, while secondary variation was associated with temperature and dissolved oxygen. Ecological risk assessment showed that sites with elevated nutrient concentrations exhibited higher RQ values, with the worst-case metric (RQmax) indicating moderate to high risk in several systems. Overall, nutrient enrichment—particularly phosphorus—and reduced water clarity were strongly linked to ecological condition, highlighting the need for targeted nutrient management at the watershed scale.