Agricultural intensification has stimulated the economy in the Guayas River basin in Ecuador, but also affected several ecosystems. The increased use of pesticides poses a serious threat to the freshwater ecosystem, which urgently calls for an improved knowledge about the impact of pesticide practices in this study area. Several studies have shown that models can be appropriate tools to simulate pesticide dynamics in order to obtain this knowledge. This study tested the suitability of the Soil and Water Assessment Tool (SWAT) to simulate the dynamics of two different pesticides in the data scarce Guayas River basin. First, we set up, calibrated and validated the model using the streamflow data. Subsequently, we set up the model for the simulation of the selected pesticides (i.e., pendimethalin and fenpropimorph). While the hydrology was represented soundly by the model considering the data scare conditions, the simulation of the pesticides should be taken with care due to uncertainties behind essential drivers, e.g., application rates. Among the insights obtained from the pesticide simulations are the identification of critical zones for prioritisation, the dominant areas of pesticide sources and the impact of the different land uses. SWAT has been evaluated to be a suitable tool to investigate the impact of pesticide use under data scarcity in the Guayas River basin. The strengths of SWAT are its semi-distributed structure, availability of extensive online documentation, internal pesticide databases and user support while the limitations are high data requirements, time-intensive model development and challenging streamflow calibration. The results can also be helpful to design future water quality monitoring strategies. However, for future studies, we highly recommend extended monitoring of pesticide concentrations and sediment loads. Moreover, to substantially improve the model performance, the availability of better input data is needed such as higher resolution soil maps, more accurate pesticide application rate and actual land management programs. Provided that key suggestions for further improvement are considered, the model is valuable for applications in river ecosystem management of the Guayas River basin.