Wastewater treatment plants (WWTP) effluents can release microbiological pollutants, including the intI1 gene (integrases of class 1 integrons), which has been proposed as a target for monitoring anthropogenic pollution in surface waters. This gene has also a strong correlation with antibiotic resistance, making of it an important proxy to evaluate the level of genetic contamination in aquatic environments. he ecological factors that influence the abundance and dynamics of intI1 within natural water bodies are largely unknown. To better understand the fate of class 1 integrons in aquatic systems, we resorted to classical limnological monitoring of intI1 over multiple years. We also conducted experiments to elucidate the impact of Daphnia grazing on its abundance. The monitoring of different size fractions of the Lake Maggiore microbial community has shown a particle-bound life-style for intI1-harbouring bacteria. Most of the bacteria hosting intI1, originating from both a wastewater effluent that discharges intro Lake Maggiore and lake water itself, grow on particulate substrates in open waters, making them particularly vulnerable to grazing by large filter feeders such as Daphnia. Daphnia grazing is independent from the origin (lake water or wastewater) of the bacterial genera; it selectively removes bacteria that are present in aggregates or even filamentous forms from both origins. To understand if intI1 is related to viable bacteria or just DNA residues, it is important to study the persistence of class 1 integrons with their gene cassettes, which often contain antibiotic resistance genes in freshwater ecosystems.