Nanoflagellates are recognized as fundamental members of the planktonic microbial food web due to their contribution to photosynthetic fixation of carbon and phagotrophic ingestion of bacteria. Although the presence, and often dominance, of mixotrophic nutrition among phytoflagellates has been well documented within a variety of aquatic ecosystems and in a range of taxa, few studies have assessed the abundance and grazing impact of mixotrophs in comparison to their photosynthetic and heterotrophic counterparts across seasons at multiple depths. Abundance and, as appropriate, bacterivory of phototrophic, heterotrophic, and mixotrophic nanoflagellates were quantified at three depths over a 15‐month period in Lake Lacawac (Pocono Mountains, Pennsylvania, U.S.A.) via microscopic analysis of ingested bacterial surrogates. The absolute and relative abundances of all nanoflagellate trophic groups varied with season and depth, likely as a result of differences in physiological tolerance. Whereas the abundance of phototrophic and heterotrophic nanoflagellates varied with depth in both the presence and absence of thermal stratification, mixotrophic protists were evenly distributed throughout the water column during mixis. The abundances of phototrophic and mixotrophic protists were significantly correlated, but only in surface waters during periods of thermal stratification. Grazing rate and consequent impact by bacterivorous nanoflagellates varied with depth across season, particularly during thermal stratification. Mixotrophic bacterivory exceeded that of heterotrophs in the epi‐ and metalimnion during stratification, removing an estimated maximum of 80% of the bacterial standing stock d−1. The relative contribution of heterotrophic nanoflagellates to community bacterivory increased with depth, even during mixis, and dominated the grazing impact in the hypolimnion.