High-elevation lakes are recognized as being sensitive to changes in climate, atmospheric deposition, and other global effects. Most studies of high-elevation lakes in the North Cascades have used a landscape-scale approach to describe aquatic systems, but smaller scale research is needed to examine natural variation in these types of lakes. We conducted a watershed-scale study encompassing four close-proximity lakes near Mt. Baker (Whatcom Co., WA) in order to examine the variation in phytoplankton and water quality in these lakes. The lakes were sampled weekly during the ice-free season of 2012 to measure seasonal changes. Chlorophyll-a levels were < 2.0 µg L-1, confirming the oligotrophic nature of these lakes. Nitrogen limitation was indicated by median DIN:TP < 3 at all sites, along with significant correlations between chlorophyll-a and nitrogen. The phytoplankton were represented by 49 genera (79 unique taxa), which was comparable to landscape-scale studies of North Cascades lakes. Ordination of phytoplankton samples separated the lakes into two groups: one group dominated by diatoms and the other dominated by Chlorophyta, Cyanobacteria, and Ochrophyta. The diatom group was associated with lower water temperatures and total nitrogen concentrations, and higher pH, dissolved oxygen, nitrate, and phosphate concentrations. Results aligned with differences in the lakes' external physical environments, including lakeshore vegetation and ice-melt timing. Our results demonstrated that close-proximity, high-elevation lakes can differ in phytoplankton and water quality, which should be taken into account when evaluating larger scale patterns across multiple watersheds and mountain ranges.