The optimisation of water purification with biological activated carbon (BAG) is described. Procedures are suggested to control biofilm growth and to use bio-indicators to predict TOC (total organic carbon) and COD (chemical oxygen demand) removal efficiencies. Empty bed contact time (EBCT) was a major physical control parameter. Dissolved oxygen (DO), pH and nutrients of the influent were controlled according to the abundance of bacteria, protozoa and rotifers. Numbers of micro-organisms in BAC beds were determined. Certain genera of ciliated protozoa, representing healthy environmental conditions, were employed as biological indicators for system performance during biological regeneration of exhausted granular activated carbon (GAG). There was a strong positive correlation between the abundance of some protozoa in the liquid phase of the BAC bed and COD concentration in the effluent. Mathematical spreadsheet models were constructed to estimate COD removal efficiency of BAC filters with different loading rates, DO, pH, nutrient requirements and populations of micro-organisms.