A periphyton biofiltration system of mariculture effluents was studied to identify ecological processes and management procedures that strongly affect the biofilter functioning, in order to attain optimal biomass production and nutrient removal. The multivariate statistical technique of factor analysis allowed reducing the large amount of data available into three main factors. The first factor, which accounted for 49% of the overall data variability, was herein called “biological activity” as it represents the joint effects on the variables measured of photosynthesis, N and P uptake, respiration and decomposition of organic matter. The second and third factors were “autotrophic biomass density” and “nitrite and phosphate uptake/release balance”, which, respectively, accounted for further 20% and 14% of the data variability. A conceptual model, describing the functioning of the periphyton biofilters, revealed a delicate equilibrium among the different processes, whose understanding help to manage the biofilters towards optimal production of periphytic biomass and nutrient removal. Raising flow rate raised the overall nutrient uptake rate but reduced uptake efficiency and diluted nitrifying particles. A reduced flow rate led to sedimentation of organic particles, decomposition and nutrients re‐mineralization. Apparently, control of water flow and nutrient content, periphyton substrate area and the cleaning of the effluent supply system are key management elements for the operation of a periphyton‐based biofilter system that maximizes both periphyton biomass production and nutrient removal.