When applying New Institutional Economics (NIE) to empirical studies one is confronted with typical problems of operationalization. To illustrate some of these problems, this paper utilizes a comparative institutional analysis of the German Water and Soil Associations and alternative governance structures for watercourse maintenance. It gives a brief introduction into the logic behind this approach (1) and discusses some terminological problems of NIE (2). The next sections illuminate the domain of watercourse maintenance (3), and the different governance structures organizing this function (4). Subsequently, four evaluative criteria are selected and explicated (5), and the operationalization and application of the criterion 'institutional congruence' is exemplified (6). Finally, section 7 sums up.