Methanogenic fermentation involves a natural ecosystem that can be used for waste water, treatment. This anaerobic process can have two locally stable steady-states and an unstable one making the process hard to handle. The aim of this work is to propose analytical criteria to detect hazardous working modes, namely situations where the system evolves towards the acidification of the plant. We first introduce a commonly used simplified model and recall its main properties. To assess the evolution of the system we study the phase plane and split it into nineteen zones according to some qualitative traits. Then a methodology is introduced to monitor in real-time the trajectory of the system across these zones and determine its position in the plane. It leads to a dynamical risk index based on the analysis of the transitions from one zone to another, and generates a classification of the zones according to their dangerousness. Finally the proposed strategy is applied to a virtual process based on model ADM1. It is worth noting that the proposed approach do not rely on the value of the parameters and is thus very robust. (C) 2009 American Institute of Chemical Engineers Biotechnol. Prog., 25: 643-653, 2009