Abstract:
Ever-increasing population and the rapid increase in the development of Lilongwe City has led 
to high increase in water demand. Understanding the complexity of the hydrogeochemical 
process, which controls the variability of the groundwater composition, is vital in groundwater 
resource management for both scientific community and policy makers. This study 
characterized deep aquifers and defined hydrogeochemistry with hydrogeological settings 
within crystalline basement complex rocks of Lilongwe. Study is an quantitative research 
design which used an experimental research approach using both purposive sampling in 21 
deep wells and simple random sampling on 50 shallow wells to collect groundwater samples. 
Due to microbial analysis requirement only shallow well samples were used for microbial 
analysis since deep wells could meet the required time of sampling duration of within 24 hours 
of collection. Statistical analysis was done using IBM SPSS, chemical plots was done using 
Aquachem 14 and spatial maps was done using ArcGIS. Aquifers were characterized into 
fractured aquifers and weathered aquifer. Fractured aquifers have of low to high yield and 
transmissivity of low to medium. Weathered aquifers have very high yield and very high 
transmissivity. Aquifers are defined by the concentration of Ca2+-HCO3-, indicating influence 
of recharge through rainfall. Presence of Na+ and SO42- shows mixing of this fresh groundwater 
with older water. Aquifer chemistry is controlled by the precipitation of oversaturated minerals 
with increasing TDS, ion exchange and simple dissolution.  Deep fractures are spatially related 
to the dominance of Na+ and SO42-, shows presence of deep percolation and dominance of 
Ca2+, Mg2+ and HCO3- relates to shallow fractures. Ca-HCO3 is the most dominant water type 
among; Na-K-Cl-SO4, Na-K-Cl-SO4 and Ca-SO4. Dominance Ca-HCO3 water shows presence 
of recently recharged groundwater within basement aquifers. Groundwater flow system within 
the basement aquifers occurs in; local, intermediate and regional. Local groundwater flow 
system is associated with weathered zone. Intermediate system occurs in both the weathered 
and fractured zones. Regional groundwater flow system is deep, occurring mainly in the deep 
fractured basement aquifer. All groundwater chemical parameters were within the 
recommended standard of MBS 2017 and WHO 2018 standard for domestic use. Basement 
aquifers are within the FAO 1994 irrigation water index requirement for irrigation use.