The focus of this paper is to investigate the ability to assess the flow exchanges between the matrix and the conduits in two karstified watersheds (Aliou and Baget, Ariège, France) using the KarstMod modeling platform. The modeling is applied using hourly and daily time series. First, the flow dynamics between the conduit and the surrounding matrix are described on a rainfall event scale (i.e., a few days). The model allows us to describe a physical reality concerning the flow reversal between matrix and conduit when there is a significant rainfall event. Then, the long-term trends (i.e., inter-annual) in the matrix water level are evidenced using the moving average over shifting horizon method (MASH). The mean water level in the matrix dropped about 10% to 15% since the late 1960s. Also, the matrix recharge has been delayed from February in the late 1960s to April since the 1990s. Moreover, the contribution of the matrix in the total spring flow is estimated though mass balance. It is estimated that the annual matrix contribution in the total spring flow is about 3% and it can increase to up to 25% during periods with low rainfall.