Dynamic Energy Budget (DEB) theory provides a powerful framework for interpreting toxicity data, but is not broadly applied in ecotoxicology yet. One of the reasons is the fact that estimation of DEB parameters from experimental data is certainly not a trivial affair. Almost every data analysis raises new questions, which require the formulation of specific mechanistic hypotheses. These hypotheses should be translated into model adaptations, which can subsequently be tested on the data set. In this paper, we demonstrate this procedure by analyzing a case study for ecotoxicity within the DEB framework. The case study we selected is a previously published data set for 4-n-nonylphenol in the polychaete worm Capitella teleta (formerly Capitella sp. I). Particular aspects of interest in this study are an apparent slow initial growth, and low-dose stimulation (hormesis) of growth and reproduction. In this publication, we explicitly discuss our deviations from the standard DEB model in terms of the underlying hypotheses, the existence of alternative hypotheses to explain the data, and how limited additional experiments can be designed to decide between alternative explanations.