In this paper, a study of the sediment transport in a complex Mediterranean watershed (i.e. the Koiliaris River Basin of Crete) consisting of temporary flow tributaries and karstic springs is presented. Both daily flow data (2005-2013) and monthly sediment concentration data (2011-2013) were used to calibrate the modified Soil and Water Assessment Tool (SWAT) model, designed to simulate the hydrology, sediment yield and water quality of ungauged watersheds, and augmented with a karst flow model in order to simulate the contribution of the extended karst to the spring discharge in the basin. The results showed good agreement between observed and model values for both flow and sediment concentration. However, since no data representative of high sediment concentration conditions were available, such as during extreme flow events, an automated sediment sampling device (Sediment Trap), which allows for flow weighted sampling, has been developed and is detailed in this paper. This device is undergoing testing to ensure it can provide accurate estimates of sediment yield, especially during a flush flood event when large amounts of sediment are carried downstream. The sediment measurements will then be used to calibrate and verify the sediment transport simulations of the Koiliaris River watershed generated by the SWAT model. The sediment transport simulations and the development of the automated sampling device were part of the preliminary work for the pilot application of the “Cybersensors” infrastructure in the Koiliaris River. The Cybersensors research project aims to develop an intelligent integrated monitoring system, which will utilize electrochemical and optical sensors, and will allow for high-frequency monitoring of the physical and chemical parameters of a river flow and thus the rapid detection of environmental change during episodic events, as well as for long term monitoring.