Exploratory data analysis on physical, chemical, and biological data from sediments and water in Lake Champlain reveals a strong relationship between cyanobacteria, sediment anoxia, and the ratio of dissolved nitrogen to soluble reactive phosphorus. Physical, chemical, and biological parameters of lake sediment and water were measured between 2007 and 2009. Cluster analysis using a self-organizing artificial neural network, expert opinion, and discriminant analysis separated the data set into no-bloom and bloom groups. Clustering was based on similarities in water and sediment chemistry and non-cyanobacteria phytoplankton abundance. Our analysis focused on the contribution of individual parameters to discriminate between no-bloom and bloom groupings. Application to a second, more spatially diverse data set, revealed similar no-bloom and bloom discrimination, yet a few samples possess all the physicochemical characteristics of a bloom without the high cyanobacteria cell counts, suggesting that while specific environmental conditions can support a bloom, another environmental trigger may be required to initiate the bloom. Results highlight the conditions coincident with cyanobacteria blooms in Missisquoi Bay of Lake Champlain and indicate additional data are needed to identify possible ecological contributors to bloom initiation.