Spatiotemporal distributions of rare microbial taxa were examined in 384 samples from the Bermuda Atlantic Time-series Study (BATS) site, in the northwestern Sargasso Sea. Sequences were partitioned into 6 mutually exclusive sets based on abundance (abundant, rare, and very rare) and frequency of detection (frequent and infrequent). Analyses of variance for taxa that were frequently present, across all levels of abundance, demonstrated environmental filtering, indicating that gradients in environmental factors, such as season and depth, drive community assembly for rare taxa, as they do for abundant taxa. All abundant nodal taxonomic units (NTUs) had spatiotemporal periods of rarity, providing a clear demonstration of the role of fluctuating reproductive success in population dynamics, and the role of rare populations as seed banks. An inverse relationship between the number of rare taxa and physical stratification indicates that transport by mixing drives increased community diversity throughout most of the year. Populations of selected copiotrophic taxa varied in episodic patterns that were not tightly entrained to season and depth, indicating that these populations are not governed by the same rules of community assembly that apply to most other taxa and may be adapted to exploit infrequent, unknown disturbances. Overall, the findings support the perspective that the success of most rare populations was driven by the same fundamental patterns of spatiotemporal variation that drove the success of dominant populations, but also indicate potentially important roles for transport by mixing and atypical life histories in determination of community composition.