Acknowledgments This research was funded by the UK Natural Environment Research Council NERC, the Department for International Development DFID-UKAID, the Economic and Social Research Council ESRC; UPGRO Grant No NE/L001888/1: towards groundwater security in coastal East Africa. Geophysical data acquisition in the Comoros was funded by the French Development Agency AFD: project GECEAU CKM1068. We acknowledge stakeholders and community members from Grande Comore, Kilwa district and Kilifi Region for their active and fruitful participation in the focussed group discussions and questionnaire surveys. We are grateful to Bonventure Obeka and Stanley Wanjala (MA Sociology students at Pwani University) for assistance throughout the project, to postgraduate and undergraduate students from the Universities of the Comoros, Dar Es Salaam, Pwani and Kenyatta and interns from the Comoros Water Directorate DGEME for assistance in field data acquisition. We thank Isaac Marobhe (University of Dar Es Salaam) for assistance and the loan of field equipment, as well as Peter Karanja Gathu (Kilifi District Water Agency), Magai Kakuru (Kilwa District Water Department), Mahabadi Boinali (Comoros Water Directorate DGEME), Youssouf Ben Abdallah (Comoros Community Representative CIGEO) and Simon Onywere (Kenyatta University) for contributions to the final workshop discussions. We also acknowledge the assistance of the British Institute in Eastern Africa (BIEA) and particularly the late Joseph Mutua for his technical and logistical expertise and untiring assistance through fieldwork in Tanzania and Kenya. We are finally grateful to the Reviewers and Editorial Board of the journal for their valuable comments and suggestions that helped improving the quality of the manuscript.Peer reviewedPublisher PD

Volcanic dykes are common discrete heterogeneities in aquifers; however, there is a lack of field examples of, and methodologies for, comprehensive in situ characterization of their properties with respect to groundwater flow and solute transport. We have applied an integrated multiphysics approach to quantify the effect of dolerite dykes on saltwater intrusion in a coastal sandstone aquifer. The approach involved ground geophysical imaging (passive magnetics and electrical resistivity tomography), well hydraulic testing, and tidal propagation analysis, which provided constraints on the geometry of the dyke network, the subsurface saltwater distribution, and the sandstone hydrodynamic properties and connectivity. A three‐dimensional variable‐density groundwater model coupled with a resistivity model was further calibrated using groundwater and geophysical observations. A good agreement of model simulations with tide‐induced head fluctuations, geophysically derived pore water salinities, and measured apparent resistivities was obtained when dykes' hydraulic conductivity, storativity, and effective porosity are respectively about 3, 1, and 1 orders of magnitude lower than the host aquifer. The presence of the dykes results in barrier‐like alterations of groundwater flow and saltwater intrusion. Preferential flow paths occur parallel to observed dyke orientations. Freshwater inflows from upland recharge areas concentrate on the land‐facing side of the dykes and saltwater penetration is higher on their sea‐facing side. This has major implications for managing groundwater resources in dyke‐intruded aquifers, including in coastal and island regions and provides wider insights on preferential pathways of groundwater flow and transport in highly heterogeneous aquifer systems.

Understanding the spatio-temporal variability in groundwater recharge is a prerequisite to sustainable management of aquifers. Spatial analysis of groundwater stable isotopes uncovered predominant controls on groundwater recharge in the Nairobi aquifer system (NAS) and the South Coast aquifer (SC), two exemplar East African aquifers relied upon by 7 million people. We analysed 368 samples for stable isotopes and basic physico-chemical parameters. The NAS groundwater isotopes are controlled by precipitation orographic effects and enriched recharge from impounded lakes/wetlands; the SC isotopes are correlated with water-table depth influencing evapotranspiration. Global Network of Isotopes in Precipitation (GNIP) data revealed groundwater recharge during months of heavy rains in the NAS, whilst the SC experiences spatio-temporally diffuse recharge. Inferred “isoscapes” show: in the NAS, (1) direct, rapid recharge favoured by faults, well-drained soils and ample rainfall in uplands, (2) delayed recharge from impounded lakes and wetlands in mid-lands, and (3) focused, event-based recharge in floodplains; and in the SC, diffuse recharge complicated by significant water-table evapotranspiration processes.