Purpose The objective of this study was to modify a sediment contact protocol to a multiwell plate exposure system which supplements measurement of the fresh weight change (FWC) using the non-invasive effective quantum yield of energy conversion at photosystem II (PS II) reaction centres (Y(II)) in parallel. Since Y(II) is a functional parameter and FWC represents a whole-plant structural response, the determination of a more pronounced response in one of these parameters may hint at the mode of action of contaminants. By the observation of Y(II) at different time points, extrapolation of effect development over time may be gained from modelling. Material and methods An established sediment contact protocol was adapted to an exposure in multiwell plates. During exposure, the Y(II) of exposed Myriophyllum aquaticum was measured using an imaging-pulse amplitude-modulated chlorophyll fluorometer. At the end of the 13-day exposure, the FWC was determined and the IC 50 for FWC and Y(II) was estimated using concentrationresponse modelling. A concentration-time-response model was used to describe the effect development on Y(II) over time. This protocol was applied to natural sediments and to artificial sediments which were spiked with different contaminants. Results and discussion It was shown that for the PS II inhibitor atrazine, the IC 50 was four times lower on the Y(II) compared to the value for the FWC. In contrast, for the acetolactate-synthase inhibitor metsulfuron methyl, no effect on the Y(II) of exposed M. aquaticum could be found, while a 100% inhibition in FWC was detected. For dinitro-ocresol, a decoupler of oxidative phosphorylation, the IC 50 for the FWC and the Y(II) were of the same order of magnitude. These results are in agreement with the current mode of action understanding and show the potential of this method to interpret differences in determined IC values as mode of action dependent. Moreover, a clear decrease in estimated I Y(II),tx C 50 values by the end of the 13-day exposure was found for atrazine. This strengthens the hypothesis that effects of contaminants in sediment are not immediately evident but may evolve over time.Conclusions With the miniaturised sediment contact assay, mode of action dependent differences in IC values on the Responsible editor: Marc Babut Electronic supplementary material The online version of this article (FWC and the Y(II) could be determined. Based on results from the concentration-time-response modelling, it could be assumed that during the 13-day exposure all contaminants may not fully exert their effects. Since investigated natural sediments did not show inhibitions on Y(II), while pronounced effects on the FWC were found, the FWC may also be worthwhile to be studied over time.