The circumalpine lake side settlements are a unique source of detailed information on the past. Nevertheless, little has been published by now on why the organic matter (fumier lacustre) in these settlements has been preserved and how exactly this happened. It is, therefore, necessary to closely explore the decomposition of organic matter under different conditions. We present data from the literature and a decomposition model simulating the outcome of different archaeological hypotheses and comparing the result with the actual archaeological record. We conclude that different scenarios of deposition should result in clearly discernible and measurable features in the archaeological record, whose presence or absence allows deducing the mode of deposition. The best conditions of organic preservation are to be expected under such conditions where a large organic input happens in shallow still water. Seasonal flooding and a later rise in lake level can also result in good preservation but imply a greater loss through mechanical erosion and in many cases clear preservation gradients within the deposits. The theoretical outcomes presented here find clear analogs in the archaeological record.