Although groundwater is an important source for drinking and irrigation water worldwide, particularly in arid countries, they have been paid little attention to their contamination with microcystins (MCs) compared to surface water. Our study is the fourth one reporting existence of MCs in groundwater due to surface-water and groundwater interaction. Dissolved MCs in groundwater were found with higher concentrations in summer (0.1 to 0.84 μg L-1) than in winter (0-0.06 μg L-1), in association with MCs detected in nearby surface Nile water. The chronic daily intake (CDI) of MCs for both adults and children (0-0.003 μg kg-1 body weight d-1) in groundwater were lower than the chronic reference dose (RfD, 0.003 μg kg-1 body weight d-1) during winter, with hazard quotient less than 1. Conversely, CDI values exceeded the reference dose during summer for both adults (0.005-0.024 μg kg-1 body weight d-1) and children (0.012-0.05 μg kg-1 body weight d-1), with hazard quotient greater than 1. This indicates that MCs concentrations in these groundwater wells might pose adverse health effects to both adults and children during summer, but not during winter. The study provides evidence for the risk of cyanotoxins in groundwater close to cyanobacteria-contaminated surface water. Therefore, regular monitoring for cyanotoxins in groundwater supplies used for drinking-water should be undertaken when cyanobacteria bloom events are noted in nearby surface waters.