We studied the spatiotemporal dynamics of ammonia-oxidizing archaea (AOA) in 2 deep and large peri-alpine lakes (Annecy and Bourget; oligotrophic and mesotrophic, respectively) over 2 years. Monthly, we characterized the structure, richness, and abundance of AOA populations in the epi- and hypolimnion using DGGE and qPCR of the archaea-specific amoA gene. Clear vertical patterns were observed in both lakes, with greater values for AOA richness and amoA gene abundance in the hypolimnetic layers. AOA community composition and structure was much more stable throughout the year in Lake Bourget than in Lake Annecy. In the upper layers, AOA communities displayed seasonal succession patterns and had greater abundance in winter. The temporal structure showed more pronounced seasonal patterns in Lake Annecy than in Lake Bourget. In the deeper layers of both lakes, AOA relative abundance showed no clear temporal pattern. Temporal changes in amoA gene composition were correlated with changes in the archaeal 16S rRNA gene in surface waters. Changes in the structure of both genes were not significantly correlated in the hypolimnion suggesting that the temporal changes in the structure of archaeal communities in the deeper waters might be globally driven by the dynamics of heterotrophic archaea and not archaeal ammonia oxidizers. None of the many environmental variables we measured explained significant amounts of variation in AOA community structure and richness; thus, other factors and processes may exert selective pressure on the structure of these communities. Nevertheless, archaeal amoA gene abundance varies with water temperature (negative correlation) and with nitrate concentration (positive correlation). Our study is the first to show that archaeal amoA gene abundance is correlated positively with silica and negatively with total nanoflagellate abundance. This suggests that AOA could play a significant role in silica dissolution and regeneration, and points to the possible influence of predation on AOA abundance.