Despite the fact that the increased use of elements linked to the Anthropocene is frequently assumed to lead to an increase in the concentrations of the elements in surface waters, temporal trends of trace element (TE) concentrations have rarely been checked. A temporally extended, traceable dataset of TE concentrations in the waters of Lake Geneva, Switzerland (1996–2015) has been used here to explore methodological and data treatment issues that arise when attempting to rigorously determine temporal trends in freshwater TE concentrations. The trace elements studied (Cd, Co, Gd, Mo, Pb, Sb, Sr) have been chosen to cover a wide range of chemical and utilisation conditions. We show that detecting temporal trends from monitoring program data is feasible, even when trends are weak, provided that rigorous data treatment methods are applied. Aspects related to the effect of data quality are discussed in detail. However, ascertaining the statistical significance of any trends calculated remains a difficult issue. With the exception of Co and Sr, that show no significant changes, and Pb, that shows a general decrease, concentrations in lake waters of the trace elements considered have increased significantly, particularly between 2006 and 2015.