A reference lake, Otisco Lake, NY, was selected to evaluate rehabilitation initiatives to mitigate severe cultural eutrophication of Onondaga Lake, NY. Onondaga Lake was mesotrophic before European development. The reference lake selection was based on an analysis of paired monitoring datasets for temperature, fluorometric chlorophyll (Chl(f/a).) and dissolved oxygen (DO), collected daily by robotic profiling platforms for the spring to fall interval of three years. The various metrics of trophic state documented here for Otisco Lake represent reasonable informal interim goals for the rehabilitation of the cultural eutrophication of Onondaga Lake. The use of Otisco Lake as a reference site is supported by its similar stratification/mixing regime and mesotrophic state, in addition to its proximity (similar to 25 km) and similar morphometry with Onondaga Lake. Strong contrasts in water quality manifestations of trophic state are depicted in Onondaga Lake, including higher Chl(f/a). (3.5-fold), prevalence of blooms, greater deviations of DO from saturation conditions, much lower minimum DO values at fall turnover in the upper layers and a higher volumetric hypolinmetic oxygen deficit (VHOD; 1.55-fold). Advantages of the fine vertical and temporal scale capabilities of the monitoring platforms are demonstrated in characterizing these and other limnological features. Continued robotic monitoring at Otisco Lake as a reference site and Onondaga Lake through the rehabilitation program will support ongoing comparisons to assess progress and will help engage stakeholders in the process.