Freshwater ecosystems occupy <1% of the Earth’s total surface area but provide an array of ecosystem services. However, these ecosystems are threatened by multiple stressors, including overexploitation, infrastructure developments, habitat alteration, and alien species introductions. The magnitude of these threats varies in different water bodies, requiring site-based conservation actions. In this paper, we aimed at developing a priority index (CPIw) that can be used to inform conservation managers in prioritizing the selection of a waterbody for site-based fish conservation purposes. We used data on distribution, diversity, and conservation status of fishes of Uganda, which were retrieved from the Global Biodiversity Information Facility (GBIF) and International Union Conservation for Nature (IUCN) databases. In the index, we incorporated the species richness, surface area of a waterbody, species rarity, and species IUCN status. A total of 288 fish species were recorded in 81 waterbodies (7 large lakes, 37 small lakes, and 37 rivers). Of these species, 110 were only found in large lakes, followed by rivers (19) and small lakes (6). Despite the higher species richness in large lakes relative to small lakes, the latter recorded significantly higher CPIw compared with the former (t = -2.8, df = 30, p-value = 0.008, d=0.7). This observation is consistent with the expectation, given the low ecological substitutability for the species and higher levels of exposure to human-induced threats in small water bodies compared with large systems. Therefore, we suggest that in situations where resources are limiting, small water bodies need to be given much attention, although we do not suggest ignoring water bodies with low CPIw values.