Rainfed agriculture is dependent on rainfall and runoff patterns, especially in lowland areas that rely on pumping operation to remove excess water from the drainage network. Polder areas are extremely vulnerable to saltwater intrusion and subsequent soil salinization driven by rising sea levels and accelerated by climate change. The aim of this paper is to reconstruct the recharge and discharge pattern in the Vidrice polder, a drainage canal network within the Neretva River Delta agroecosystem used to collect the surface and subsurface runoff from the agricultural land and saltwater infiltration through the aquifer. Water regime data are collected over an 18-month period of real-time monitoring at 15 min intervals on three stations along the primary drainage canal and one station at the secondary canal. Analysis of water level flashiness in the Vidrice polder using the Richards-Baker flashiness index (R- Bindex) indicates that daily pumping of water infiltrated in the canal network is sub-optimal: discharge fluctuates significantly more than recharge, by 46% on average, resulting in unnecessary lowering of the water level in the drainage network. The results show that the correlation between the intensive rainfall events (>10 mm/day) and the recharge rates can be used to modify the daily pumping operation and maintain high freshwater levels in the canal network to increase the resistance to infiltration and reduce saltwater intrusion into the polder.