An approach in determining ecosystem integrity and stress on ecosystem level is to assess processes within ecosystems. The aim of the present study was to evaluate the potential use of an in situ assay with immobilized Chlorella vulgaris as an indicator of effects on ecosystem functioning with regard to primary production. The herbicide linuron, applied in concentrations of 20, 60, and 180 μg linuron/L, was used to induce direct effects on primary producers. Direct and indirect changes in structure and function within outdoor model ecosystems of 3 m3 were monitored. The intermediate and highest concentration of linuron caused a decline in growth of the macrophyte Elodea sp., resulting in a significant increase of concentrations of nutrients. The increase in concentrations of nutrients caused an indirectly stimulated growth of immobilized C. vulgaris at the intermediate concentration, whereas similar concentrations of nutrients, at the highest treatment, did not stimulate Chlorella growth. It appeared that the direct effect of linuron on C. vulgaris growth was masked by nutrient availability at the intermediate but not at the highest linuron concentration. The observed immobilized algal growth was an accumulated effect of toxic and trophic pressures within the ecosystem, resulting in an integrative endpoint to detect actual impairment of ecosystem function.