Pharmaceuticals are substances designed to have a biological effect in humans. Their presence in the environment, especially in surface waters, is of increasing concern because of their potential risk to non-target species. A large number of pharmaceuticals are on the market; for example, approximately 2,000 active ingredients are approved in Europe, and many of them have already been detected in surface water. It is therefore crucial to select the substances that may do the most harm to the environment prior to performing measurements and extensive risk assessment. In the present study, a method to determine a list of pharmaceuticals to survey in surface water is proposed. Inclusion of substances on the list was based on a screening procedure, the analytical feasibility, and previous knowledge of pharmaceuticals detected in water. The screening procedure proposed here is an improvement on the standard procedure of the European Medicine Evaluation Agency (EMEA). It is designed to decrease the number of pharmaceuticals to be evaluated in a stepwise manner, thus decreasing the number of data necessary for the evaluation. We applied our approach to determine a list of 37 pharmaceuticals and four hormones to survey in a specific region of Switzerland, the Lake Geneva area, and discussed the advantages and weak points of the method.