Allelopathy, here defined as biochemical interactions between aquatic primary producers, has always been intriguing as a process explaining the dominance of certain plant or algal species over others. Negative chemical interference has been invoked as one of the steering mechanisms behind mutual dominance of either submerged macrophytes or phytoplankton in shallow eutrophic lakes. Yet, despite much effort, convincing evidence for allelopathic interactions in situ is still missing. Also, laboratory approaches often lack reality. Inspired by a series of talks at the Shallow Lakes 2005 meeting in Dalfsen, the Netherlands, we argue that there is circumstantial but strong evidence that allelopathic interference between submerged macrophytes and phytoplankton may indeed exist in aquatic ecosystems despite the problems associated with research in this field. We first discuss experimental approaches combining laboratory and field studies, based on examples presented at this meeting. We then discuss the impact of nutrient status of both producing and target organism and biotic factors such as herbivory or pathogens that might affect allelopathy. Further topics are the potential seasonality of effects and the species-specificity of certain allelochemicals. We conclude with some thoughts why a final proof for allelopathy in situ might remain difficult or even inaccessible in some cases, and why we nevertheless should not abandon this idea.