An aquatic indoor microcosm was used to study effects of the pesticides parathion-methyl and prometryn on phototrophic flagellates (Cryptomonas sp.) and predatory ciliates (Urotricha furcata). Parathion-methyl caused effects to flagellates and ciliates at the range of low mg L(-1), regardless of whether the organisms were exposed separately or combined in the multi-species test system. Prometryn caused effects on the flagellates at low microg L(-1) concentrations, resulting in a NOEC of 6.9 microg L(-1) in the single-species test and a NOEC of 15.2 microg L(-1) in the multi-species microcosm. For ciliates the NOEC decreased by factor 145 in the multi-species test compared to the NOEC of 2.2 mg L(-1) in the single-species test when exposed to prometryn. The lower NOEC for ciliates exposed to prometryn in the microcosm was most likely caused by an indirect effect due to reduced availability of flagellates as food. The measurement of nutrient concentrations in the test media and organisms facilitated the modelling of effects. The presented aquatic indoor microcosm is considered as a tool which could be standardised and applied as an instrument to provide data for higher tier risk assessment.