Irrigation practices may have adverse impact on aquatic ecosystems. Quantification of such impacts is possible only if a condition of an aquatic ecosystem is known before the impacts started. This study attempted to simulate the reference hydrologic regimes of three coastal lagoons in southern Sri Lanka, two of which are currently receiving return flows from upstream irrigation scheme. The lagoon that does not receive irrigation drainage flows is considered to be a reference wetland. The simulation of its water volumes and levels was carried out using a daily water-balance model. The model assumed that a lagoon may be described as a reservoir, which is separated from the sea by a sand bar. The simulated water levels in a reference lagoon were then modified to describe water-level fluctuation in the other two lagoons. This modification uses a spatial interpolation approach based on duration curves and incorporates information received from local farmers. The probable changes caused by irrigation drainage flows to two lagoons can be illustrated by duration curves of observed and simulated water levels.