Stream degradation increases with high anthropogenic activity and climate variability, while declines occur in biodiversity. However, few studies have been undertaken on tropical waterways, a major impediment to biodiversity conservation. The present study was conducted on 95 relatively pristine small streams in Eastern Thailand with 10 reasonably uncommon species of balitorid fishes. Measurements were made of 21 physical and chemical factors and the substrate particle size. Stepwise regression identified the direct importance of substrate particle size and nitrate on the species’ richness of balitorids, whereas its abundance was negatively related with iron concentrations. A Canonical Correspondence Analysis identified three fish groups: the 1st group was negatively correlated with ammonia and positively correlated with dissolved silica, the 2nd group was positively correlated with substrate particle size and negatively correlated with stream ambient temperature and ammonia concentration, and the 3rd group was negatively correlated with low dissolved silica, respectively. The results of this study may indicate the vulnerability of balitorids under climate warming and anthropogenic pressure that alter the water physicochemical factors and river degradation including the substrate type. Thus, a conservation framework should be provided regarding the limits for water temperature, ammonia, and iron in Thailand’s Water Quality Criteria to better protect its freshwater ecosystem. Balitorid is a potential bioindicator for evaluating the river temperature effect in combination with ammonia nutrient stressors as long as the way-of-life habits of the species are taken into account.