Background: Whole sediment contact tests provide realistic exposure scenarios, but the inherent properties of sediments may play a significant role in organism's response and interfere with result interpretation. Recently, a sediment contact test with a rooted aquatic macrophyte Myriophyllum aquaticum has been standardized. The present study aims to distinguish between effects of basic sediment properties and sediment-bound pollutants on M. aquaticum growth and evaluate the method as a tool in sediment quality assessment. Tests with artificial sediments with different organic matter, sand and clay content, as well as freshwater sediments with different levels of contamination were conducted. Results: Results were based on comparison to the standard artificial control sediment. Organic matter content and grain size distribution in different variants of artificial sediments significantly affected M. aquaticum growth. Growth was impaired in formulations with low (1%) and high (10%) organic matter content, while better growth of plants compared to control was recorded in artificial samples with higher fine particles content. Because of the presence of unmeasured pollutants in freshwater sediments and inherent sediment properties, results of the M. aquaticum sediment contact tests were not always in accordance with the results of chemical analysis. Whorl, shoot and root parameters had different variability and showed a particular growth pattern in natural sediments. If the threshold of 20% for sediment toxicity is applied, then about 60% of tested natural sediments may be considered as toxic. As sediment structure may influence plant growth, this interpretation may be false as the physico-chemical properties of the control sediment used for comparison are considerably different from the properties of natural sediments. Conclusions: Since inherent properties showed a significant effect on plant growth, the use of suitable controls more similar to tested natural sediments is advisable. To avoid over-, but also under-estimations, the use of the strict toxicity threshold of 20% or even higher inhibition for this test can be recommended, provided the statistical power of the test is high. The results of this study might contribute to the ongoing process of including effect-based methods in water quality monitoring under the Water Framework Directive.