Shallow polymictic lakes are very abundant in many regions of the world, they are more numerous than deep lakes and are of great importance especially in densely populated areas even when small. Their ecology differs from stratified lakes in many ways. During the eutrophication process, lakes may change from a clear water, macrophyte dominated state to an algal dominated state, a process known as the concept of ‘alternative stable equilibria’. The usefulness of this concept as a descriptor for the eutrophication process and as the basis for rehabilitation of lakes is tested on long-term data from two contrasting case study sites using a novel multivariate bubble-plot technique. In one case the concept proved to be useful and successful while it could not be applied to a large shallow turbid lake. The equilibrium concept is then generalised using further examples. Shallow lakes which are either macrophyte dominated or light limited because of high inorganic background turbidity have ratios of total phosphorus (TP) to algal Chlorophyll-a at or below 3:1. Deep oligotrophic or algal dominated lakes in contrast exhibit ratios between 3:1 and 1:1. Alternative stable equilibria of macrophyte or algal domination can occur within the same water-body at various locations, at different times of the year or during trophic development.