The practical and conceptual challenges faced by the analysis of trace elements present in natural waters are not merely, as is often thought, an endless race towards lower detection limits or to the development of techniques allowing the determination of any possible chemical species formed by all chemical elements. Rather, as discussed in this paper, they include the development of (i) robust, cheap, and reliable methods that could also be used by laypeople (the experience gained in the development of field kits for As is discussed as an example from which similar developments for other elements may be drawn); (ii) more environmentally-friendly methods (the current guiding criteria probably being too simplistic); and (iii) methods making it possible to follow diel concentration changes and sharp concentration variations caused by the probable increase of heavy rainfall events. This paper also claims that neither the measurement of total concentrations (reliable methods are lacking for many elements of the periodic table of trace elements, as illustrated through the cases of Bi, Te, and Sb), nor chemical speciation analysis, are as mature as often thought. In particular, chemical speciation studies demand the development of a better, comprehensive conceptual framework. A trial is carried out to lay the basis of such a framework.