This dataset includes data of the freshwater crab genus Geothelphusa (Decapoda: Potamidae), their environmental parameters and stream indicators in eastern and southern Taiwan. This dataset is the result of 146 surveys (sampling events) of freshwater crab species and stream environment from 2013 to 2015 in 42 sampling sites throughout Taiwan, and a total of 12 species and 1,006 crabs of the Geothelphusa were recorded. The crab data include ‎existence or not, carapace width, carapace length, wet weight and sex. The stream environmental data include water temperature, pH value, dissolved oxygen, conductivity and three indicators (River Pollution Index, RPI; Water Quality Index 7, WQI7; citizen Qualitative Habitat Evaluation Index, cQHEI).