Inland waters, despite covering less than one percent of the Earth's surface, play a crucial role in biochemical processes due to their significant spatio-temporal variability and seasonal patterns of organisms like phytoplankton and cyanobacteria. Diatoms, a key group of photosynthetic microorganisms, need dissolved silica for their growth, which can affect the nutrient dynamics and structure of aquatic ecosystems. This study is exploring the impact of dissolved silica addition on the structure and functions of lake microbial communities, particularly diatoms. Diatoms are unicellular photosynthetic silicified organisms that require silicon to build their cell walls. Thus, silica availability is important in the regulation of diatom growth, as well as in the structure and dynamics of lake phytoplankton communities. A mesocosm experiments from April to late-August was used to study the effect of dissolved silica addition on the phytoplankton community. Meta-transcriptomics on polyA-enriched samples was used to identify expressed eukaryotic genes and evaluate the metabolic pathways involved in photosynthesis and silica uptake. Meta-transcriptomic analysis revealed metabolic changes in the phytoplankton, highlighting seasonal variations and the effect of silica addition on plankton community dynamics. In particular, the relative expression levels of diatoms increased in the treatment where silicate was added. Although we found elevated relative expression of several genes in key photosynthesis KEGG modules and light capture complexes, there were important photosynthesis components missing in the data set. This included some photosystem genes and genes for the Rubisco enzyme, indicating that potentially they are encoded in the chloroplast genomes and therefore not polyadenylated. The analysis of silica transporters highlighted a significant variation in the abundance of SITs between the control and the dissolved silica treatment, revealing a dynamic response of diatoms to the availability of silica in their environment. A high expression of these transporters was also present in some dinoflagellates raising questions about their role in the digestion of diatoms or the formation of siliceous cysts. In conclusion, our study demonstrates the significant impact of dissolved silica on the metabolic pathways and community structure of lake phytoplankton, particularly diatoms, and underscores the complex relationship between silica availability and phytoplankton dynamics in freshwater ecosystems.