Water quality is an important factor to consider when attempting to reconcile mathematical optimisation modelling with the physical reality of water-resource systems. In particular, when the greater part of water resources in supply systems comes from artificial reservoirs, as in Mediterranean regions, a simplified approach based on the attribution of the trophic state of reservoirs can be developed to consider water quality in the optimisation model. Experimental studies have demonstrated that a measure of the trophic state can be given by the Trophic-State Index (TSI), which is evaluated by chlorophyll-a concentration. When certain families of microscopic phytoplanktonic algae produce algal toxins during eutrophication, limitations on resource use based solely on TSI values may be insufficient. In this paper, a linear optimisation model is presented that includes quality indexes estimated based on both TSI and concentration density of the most toxic species of algae in reservoirs. The application of the optimisation model to a multi-reservoir system, located in Sardinia, Italy, highlights the impacts of using different water-quality indexes on the results of the optimisation model.