The dynamics of neuronal systems, briefly neurodynamics, has developed into an attractive and influential research branch within neuroscience. In this paper, we discuss a number of conceptual issues in neurodynamics that are important for an appropriate interpretation and evaluation of its results. We demonstrate their relevance for selected topics of theoretical and empirical work. In particular, we refer to the notions of determinacy and stochasticity in neurodynamics across levels of microscopic, mesoscopic and macroscopic descriptions. The issue of correlations between neural, mental and behavioral states is also addressed in some detail. We propose an informed discussion of conceptual foundations with respect to neurobiological results as a viable step to a fruitful future philosophy of neuroscience.