Inconsistency of seasonal monsoon weather patterns during the past several decades have a major influence on surface water management system in the in Sri Lanka. The present study aim is to analyze the changes in the inter-annual and intra-annual spatial and temporal variation of surface water flow in Sri Lanka to understand the surface runoff variation under the past climatic change. The spatially distributed hydrological model was calibrated and validated for four different discharge gauge stations in four basins and employed to simulate the natural surface runoff over the period 1975 - 2005 at daily time interval for 39 river basins. The rank-based, nonparametric Mann-Kendall statistical test was used for trend detection due to its robustness for non-normally distributed and censored data. The results confirm that seasonal runoff changes in basins completely located in dry zone are higher and mainly it is limited to 2nd inter and northeast monsoons. Basins located in the west and east show a significant increasing trend in mean annual runoff volume due to precipitation increase in the southwest monsoon to the west and northeast monsoon to the east. However, river basins located in northwest show general decreasing trend in mean annual runoff volume as inter-monsoon precipitation gets reduced. This study concludes that wet zone basins get wetter while leaving the dry zone drier during the past decades along with climate change.