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Abstract Temperate lakes experience variation in mixing and stratification that affects the distributions, activities, abundances, and diversity of plankton communities. We examined temporal and vertical changes in the composition of planktonic microorganisms (including Bacteria and Archaea) in oligotrophic Flathead Lake, Montana. Using a combination of approaches that included 16S rRNA gene sequencing and flow cytometric determination of cell abundances, we found that the microbial community was responsive to variations in stratification and mixing at time scales ranging from episodic (scale of days) to seasonal. However, the impact of such physical dynamics varied among taxa, likely reflecting taxa‐specific responses to environmental changes that coincide with stratification and mixing (e.g., light availability and nutrient supply). During the early spring, periods of relatively short‐term (< 7 d) intermittency in stratification and mixing influenced the vertical distributions of specific microbial taxa, notably including the cyanobacteria. These events highlight time scales of biological responses to high‐frequency variations associated with lake stratification and mixing, particularly during the transition to the growing season in the early spring. 

Summary Coral reefs are highly productive ecosystems with distinct biogeochemistry and biology nestled within unproductive oligotrophic gyres. Coral reef islands have often been associated with a nearshore enhancement in phytoplankton, a phenomenon known as the Island Mass Effect (IME). Despite being documented more than 60 years ago, much remains unknown about the extent and drivers of IMEs. Here we utilized 16S rRNA gene metabarcoding as a biological tracer to elucidate horizontal and vertical influence of an IME around the islands of Mo′orea and Tahiti, French Polynesia. We show that those nearshore oceanic stations with elevated chlorophyllaincluded bacterioplankton found in high abundance in the reef environment, suggesting advection of reef water is the source of altered nearshore biogeochemistry. We also observed communities in the nearshore deep chlorophyll maximum (DCM) with enhanced abundances of upper euphotic bacterioplankton that correlated with intrusions of low‐density, O₂rich water, suggesting island influence extends into the DCM.