We study the effects of toxicants on the functioning of phototrophic unicellular organism (an algae) in a simple aquatic microcosm by applying a parameter-sparse model. The model allows us to study the interaction between ecological and toxicological effects. Nutrient stress and toxicant stress, together or alone, can cause extinction of the algal population. The modelled algae consume dissolved inorganic nitrogen (DIN) under surplus light and use it for growth and maintenance. Dead algal biomass is mineralized by bacterial activity, leading to nutrient recycling. The ecological model is coupled with a toxicity-module that describes the dependency of the algal growth and death rate on the toxicant concentration. Model parameter fitting is performed on experimental data from Liebig, M., Schmidt, G., Bontje, D., Kooi, B.W., Streck, G., Traunspurger, W., Knacker, T. [2008. Direct and indirect effects of pollutants on algae and algivorous ciliates in an aquatic indoor microcosm. Aquatic Toxicology 88, 102-110]. These experiments were especially designed to include nutrient limitation, nutrient recycling and long-term exposure to toxicants. The flagellate species Cryptomonas sp. was exposed to the herbicide prometryn and insecticide methyl parathion in semi-closed Erlenmeyers. Given the total limiting amount of nitrogen in the system, the estimated toxicant concentration at which a long-term steady population of algae goes extinct will be derived. We intend to use the results of this study to investigate the effects of ecological (environmental) and toxicological stresses on more realistic ecosystem structure and functioning. © 2009 Elsevier Ltd. All rights reserved.