This paper is a contribution for validating a standard method for trace element monitoring based on transplants and analysis of aquatic bryophytes, in the framework of the EC Directive 2000/60. It presents the results of an experiment carried out to assess significant differences in the amount and variability of As, Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb and Zn in three moss species (Cinclidotus aquaticus, Fontinalis antipyretica, Platyhypnidium riparioides) and two different parts of the moss (whole plant vs apical tips). Mosses were caged in bags made of a plastic net and transplanted for 2 weeks to an irrigation canal impacted by a waste water treatment plant. Trace element concentrations were measured by inductively coupled plasma optical emission spectrometry (ICP-OES) and inductively coupled plasma mass spectrometry (ICP-MS) before and after exposure to the experimental and control sites in five samples. Enrichment factors >>2 were found for Cu, Ni, Mn, Pb and Zn in all moss species, lower in C. aquaticus, intermediate in F. antipyretica and higher in P. riparioides (the species we recommend to use). The analysis of apical tips after exposure instead of the whole plant led to (I) lower concentrations of As, Co, Cr, Fe and Zn in C. aquaticus (-7 to -30%) and of Fe and Pb (-13, -18%) in P. riparioides, (II) higher concentrations of Cu, Ni and Zn (+14 to +18%) in P. riparioides, while (III) no significant difference (p > 0.05) in F. antipyretica. Data variability after exposure was generally lower in apical tips, especially in C. aquaticus and in F. antipyretica, less in P. riparioides. In the aim of standardizing the moss-bag technique, the analysis of apical tips is recommended.