Fresh waters are among the most endangered ecosystems in the world. Practical tools to measure their biodiversity value are needed for their effective conservation. Besides species richness, other aspects of biodiversity, including the threat level of species also need to be considered. Currently, existing scoring methods for assessing the conservation value of freshwater fauna and flora assemblages are varied, and guidelines to select an appropriate method are lacking. In this paper, it is hypothesized that scores to assess the conservation value of assemblages can vary markedly according to the type of method used. To test this, four types of scoring methods were applied differing in the weight given to Red List categories and in the expression of the score, i.e. either using mean per species or the assemblage as a whole, on sets of dragonfly and macrophyte data collected from varied types of small lakes and ponds in three different countries (France, Switzerland and South Africa). The comparison of the different types of methods showed that the type of method used had a marked impact on the assessment of the conservation value of a water body: the expression per species or per assemblage as the weight given to Red List categories changed the value of a given water body. Overall, results also confirmed that the different types of methods could be applicable in different geographical areas and types of standing water bodies, independently of the original area where the method was developed. Results illustrated that, besides the species richness assessment commonly used, calculating conservation value as a mean per species is useful because it provides additional information. Overall, using methods expressed as a mean per species and coupling the Red List with other criteria gave the best performance.