The dynamic nature of the Batticaloa lagoon demands proper management to ensure sustainable use of the lagoon for the local communities' well-being and promote the district's long-term economic and social development. This lagoon receives runoff water from urban and rural areas, which might typically contain a broad range of pollutants that can affect lagoon water quality. In this context, studying the variation of rainfall and runoff which affect the lagoon is essential to ensure proper management of the lagoon. Therefore, the present study was conducted to estimate the runoff volume into the lagoon with the varying rainfall. Rainfall data and land-use patterns of the surroundings of the lagoon area were collected. Precipitation Concentration Index (PCI) was used to analyse the rainfall variability in the study area. The flow generated by rainfall and governed by catchment characteristics was calculated using the Soil Conservation Service (SCS) -Curve Number (CN) method. Regression and correlation analysis were performed using MS Excel and SPSS version 22 statistical software. The study found an increasing trend of rainfall (r=0.316, p=0.039) over the 43 years studied. According to the PCI values, nearly 39.5%, 46.5% and 14% of the years received very high concentration, high concentration and moderate concentration of rainfall, respectively. It was estimated that the maximum runoff into the lagoon was 1430.9 mm in 2011 and the minimum was 457.1 mm in 1981. Further, more than half of the rainwater received in the study area was lost as runoff (1107.1 mm), and the effective rainfall was 618.6 mm. It is also found that there are highly significant relationship between runoff and rainfall (r =0.988, p<0.01). These findings, especially the trend analysis of rainfall and runoff estimation, will be helpful in planning, designing, and managing water related projects in the Batticaloa district.