Phytoplankton species have been widely used as indicators of lake conditions, and they may be useful for detecting changes in overall lake condition. In an attempt to inventory and monitor its natural resources, the National Park Service wants to establish a monitoring program for aquatic resources in the Great Lakes Cluster National Parks. This study sought to establish baseline information on the phytoplankton and water chemistry of selected lakes in five national parks in a preliminary effort toward establishing a long-term monitoring program. Phytoplankton and water chemistry samples were collected from ten lakes in five national parks over a two-year period. A total of 176 taxa were identified during the study. Northern lakes generally had higher Shannon-Wiener diversity and clustered together in similarity. Lakes exhibited a south to north gradient of many water chemistry variables, with northern lakes having lower hardness, sulfate, turbidity, and temperature and higher dissolved oxygen. Chloride and sulfate concentrations were the variables that best explained variation among phytoplankton in the ten lakes. A monitoring plan will have to incorporate the differences among lakes, but by coordinating the effort, comparisons within and among parks and other regions will prove useful for determining environmental change.