The spread of antibiotic resistance bacteria (ARB) and their resistance genes (ARGs) represents a great concern to public health worldwide. The aquatic ecosystems are considered as hot spot for horizontal gene transfer and sediments act as a reservoir of different contaminants. However, the occurrence of agricultural versus medical ARGs in Swiss freshwater reservoirs is understudied. Consequently, in this study, we aimed to quantify broad-spectrum β-lactam and sulfonamide resistance genes (blaTEM, blaSHV, blaCTX-M, blaNDM, sul1 and sul2) and the total bacterial load (16S rRNA genes) from the total DNA extracted from the surface sediments of the Lake Brêt, Switzerland using quantitative polymerase chain reaction (qPCR). Additionally, sediment physicochemical parameters including organic matter, grain size and toxic metal were analyzed. The results highlight the widespread dissemination of blaTEM, blaSHV and sul1, which were also highly correlated to bacterial biomass and organic matter content (R > 0.75, p < 0.05). The blaCTX-M and sul2 were occasionally present and positively correlate with the concentration of Cr, Mn, Fe and Ni, linking it to agricultural practices. These findings demonstrate a fixation of last ARGs generation in the environment whereas actual antibiotic regulation tend to limit the dissemination of other ARGs in the studied lake reservoir.