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Increased lake salinity is a growing problem in and and semi-arid regions. Operational management, which is based on a reliable hydrological understanding, has the potential to reduce the lake salinity. This is the case of the salinity in Lake Kinneret (Sea of Galilee), where saline water flows into the lake through on-shore and off-shore springs. Here, we present a time-dependent flow and transport numerical model that successfully reproduces the monitored groundwater level, discharge, and salinity of the lake springs. The model utilizes a continuum approach and describes the flow through a confined saline carbonate aquifer, which interacts with the discharge lake through fractures and faults. In particular, the model investigates the hydrology around two groups of springs, Fuliya and Tabgha, along the western shore of the lake. Based on seasonal characteristics of the springs and measured boundary conditions, the two springs groups were defined as Lake Dominated Springs (LDS, Fuliya) and Aquifer Dominated Springs (ADS, Tabgha). The models of the two groups differ from each other in the distribution of fractured regions that link between the lake and the underlying aquifers. The numerical solution shows how the fractured regions affect groundwater head, spring discharge, and spring salinity. The different behavior of the LDS and ADS was reproduced with an excellent agreement between measured and calculated patterns. Differences in salinity within a group of springs are shown to be dependent on the depth of the fractured region. It was revealed that in addition to the appropriate distribution of fractured regions some adjustment in the up-stream boundary conditions is necessary to fully reproduce the system hydrology. The model has improved our understanding and provides a prediction tool for future management strategies. (C) 2003 Elsevier B.V. All rights reserved.