The soil and water assessment tool (SWAT) is one of the most widely used hydrological models. However, it has not been extensively applied in karst watersheds due to their geomorphological heterogeneity. Karst watersheds contribute up to 50% of water supply in Europe, while in South China alone, over 100 million people subsist on it. Hence, improving model performance for karst areas is an important area of research. Here, we propose a methodology based on field investigation and tracer test aimed at improving the conceptual understanding of the hydrological processes to guide the modeller. The Miaogou watershed was used as a case study to run the SWAT model using daily streamflow data from 2013 to 2016. Model calibration and validation results were found to be positive. Average R2 and Nash–Sutcliffe efficiency index (NSE) solutions for the validation period are 0.70 and 0.65 respectively. CN2 was the most sensitive parameter due to the concave shape of the basin as well as the presence of a sinkhole that conveys recharge faster to the main stream outlet via a spring. Our findings show that a field-based approach to modelling karst areas helps define watershed surface and groundwater boundaries, which is often neglected. It also serves as a secondary validation that can be applied anywhere rather than relying on computer code alone. In addition, tracer tests highlight the subterranean hydrological processes which define hydrological gains and losses necessary for model parameterization. Overall, this study establishes a positive outlook towards extensive application in other karstified regions of the world.