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Groyne system modification is described related to restoration efforts to Koggala lagoon, Sri Lanka.The large-scale unplanned sand removal at the lagoon mouth shifted the formation of sand bar towards the lagoon and made adverse effects on its ecosystem. After the removal of the natural sand bar, groyne system was constructed to avoid sand deposition in the lagoon and to protect the highway bridge (across the lagoon outlet channel) from the wave attack. The existing groyne system resulted the lagoon mouth being permanently open to sea which in turn led to many environmental problems. Groyne system modification is proposed in this study to reduce the sea water intrusion.Water budget and two-dimensional depth averaged hydrodynamic model were developed for understanding the hydrologic and flow characteristics of the lagoon. Numerical experiments was performed at lagoon mouth area for two cases: (1) existing condition and (2) proposed rubble mound groyne system condition. Comparison of results was obtained for both cases to describe flow pattern at lagoon mouth. Results further showed, the width should be reduced to a maximum of 40 m. Proposed mouth width (40 m) pushed the salting factor towards 0.5 from 0.68. Salting factor reduction with the groyne modification may result a predominant influence of fresh water which may in turn lead lagoon to a fresh water ecosystem.