Biological and environmental systems are often influenced by unknown inputs or disturbances, which makes monitoring or state estimation more delicate. In this study, the simultaneous estimation of unmeasured state variables and partly unknown inputs is considered. Only qualitative prior information on these inputs is used in the design procedure, leading to the concept of quasi-unknown input observers (QUIO). These software sensors are applied to the estimation of concentrations, flow rates and light intensity in phytoplanktonic cultures in the chemostat. Implementation and numerical tests are discussed, based on simulation and experimental data. (C) 2011 Elsevier B.V. All rights reserved.