Occurrence and fate of glyphosate, a widely used herbicide, and its main metabolite AMPA was investigated in Lake Greifensee, Switzerland. Monthly vertical concentration profiles in the lake showed an increase of glyphosate concentrations in the epilimnion from 15 ng/L in March to 145 ng/L in July, followed by a sharp decline to <5 ng/L in August. A similar pattern was observed for AMPA. Concentrations of glyphosate and AMPA in the two main tributaries generally were much higher than in the lake. Simulations using a numerical lake model indicated that a substantial amount of glyphosate and AMPA dissipated in the epilimnion, mainly in July and August, with half-lives of only ≈2−4 days which is ≫100 times faster than in the preceding months. Fast dissipation coincided with high water temperatures and phytoplankton densities, and low phosphate concentrations. This indicates that glyphosate might have been used as an alternative phosphorus source by bacterio- and phytoplankton. Metagenomic analysis of lake water revealed the presence of organisms known to be capable of degrading glyphosate and AMPA.