Acknowledgements: This blog is based on the ongoing implementation of the project “Enhancing Conjunctive Management of Surface and Groundwater Resources in Selected Transboundary Aquifers (2020 – 2026),” funded by the Global Environment Facility (GEF), through the United Nations Development Programme (UNDP), and implemented by the Nile Basin Initiative (NBI).

When it comes to water security, the greatest challenges often lie beneath the surface. Groundwater, vital for drinking, irrigation, and livelihoods, remains poorly monitored, undervalued, and largely absent from policy frameworks in many parts of Africa.

However, this is beginning to shift. A regional project funded by GEF, supported by UNDP and implemented by NBI is helping countries across the Nile Basin better understand, value, and govern their shared groundwater resources. Beyond technical deliverables, the initiative is showing how regional cooperation, knowledge building, and innovation can strengthen governance in transboundary settings.

Groundwater in the Nile Basin: From Hidden Resource to Shared Priority

Water stress is growing in the Nile Basin. Climate variability, population growth, and agricultural expansion are increasing pressure on freshwater sources. Groundwater has moved from a backup resource to a central pillar of water security.

However, managing groundwater, especially aquifers that cross borders, poses unique challenges. Aquifers are underground layers of water-bearing rock or sediment that store and transmit groundwater. These underground systems are often poorly understood and rarely covered in existing water agreements. Without shared policies or data, they remain over or poorly exploited.

Launched in 2020, the project focuses on long-term change: building trust, strengthening systems, and supporting institutions for cooperative groundwater governance.

Mapping the Way: Three Aquifers, Seven Countries

Through suitability mapping and consultations, the project identified three pilot transboundary aquifers involving seven countries:

• Kagera Aquifer (Burundi, Rwanda, Tanzania, Uganda)

• Elgon Aquifer (Kenya, Uganda)

• Gedaref Adigrat Aquifer (Ethiopia, Sudan)

For each, a Shared Aquifer Diagnostic Analysis (SADA) was conducted, bringing together environmental, hydrological, and socio-economic data. These baselines were co-developed with national experts through workshops, consultations, and technical exchanges.

Seven national inventories and assessments were completed, not just as reports, but as joint reference points for action.

Building Institutions and Strengthening Capacity

Data alone is not enough. For impact to be sustained, it must be institutionalized.

To that end, the project developed a regional groundwater database and integrated it into the NBI knowledge platform. By 2024, trained focal points in each country were actively contributing data, supporting long-term monitoring and decision-making.

The project also delivered training in Quantum Geographic Information Systems (QGIS), field data collection, field data collection, and aquifer modelling, alongside technical guidelines for transboundary aquifer monitoring. These efforts aimed to strengthen national capacity, reduce dependence on external expertise, and embed new knowledge in public institutions.

Piloting Nature Based Solutions: Managed Aquifer Recharge

As groundwater depletion worsens, Managed Aquifer Recharge (MAR) offers a promising approach. By storing rainwater or surface runoff underground, MAR restores aquifers, improves water quality, and builds resilience to drought.

Following feasibility assessments, the project selected five MAR pilot sites — two in Elgon and three in Kagera. NBI completed the design of two pilot MAR interventions; one each in Kagera and Elgon and conducted Environmental and Social Impact Assessments (ESIAs) for both. These were followed by extensive community engagement activities at the aquifer level, with particular attention given to the participation of women and youth.

This marked a significant step forward, as the lack of a transboundary standardized monitoring system and database had long hindered effective management of shared aquifers. Most notably, a Regional Action Plan was developed for the pilot aquifers, reflecting both scientific evidence and political realities, and stands as a testament to collaborative planning among countries.

Additionally, a regional monitoring network was designed for the Gedaref Adigrat Aquifer. Sudan and Ethiopia engaged in discussions on security and access, paving the way for the installation of monitoring stations. This was another important milestone in overcoming longstanding governance and data sharing challenges.

Governance in Practice: Planning Across Borders

Effective water governance in transboundary settings relies on relationships, not just rules. The project embraced this through 12 national consultations and two regional workshops, fostering dialogue and aligning priorities.

Most notably, three Regional Action Plans were developed for the pilot aquifers. These living documents reflect scientific insights and political realities and are a testament to collaborative planning between countries.

From Awareness to Ownership

To embed change, public understanding and engagement were prioritized.

Radio shows, short documentaries, and storytelling campaigns in Burundi, Rwanda, Uganda, and Tanzania helped translate complex concepts like “conjunctive use” into accessible language. Community voices, especially women and youth, featured prominently.

In 2024, two regional magazines documented 32 stories from across the pilot areas, capturing how groundwater access and governance affect everyday life.

Lessons Learned

This initiative offers valuable lessons for others working in transboundary natural resource management:

1. Start with shared understanding: A common evidence base builds trust and supports coordinated action.

2. Adapt to context: Flexibility helps navigate shifting priorities and institutional capacity.

3. Invest in systems, not just studies: Strengthening national institutions ensures sustainability.

4. Center people in the process: Groundwater governance is about communities, and their stories matter.

Conclusion

By prioritizing knowledge, cooperation, and adaptive governance, this project is laying the groundwork for a more inclusive and resilient water future in the Nile Basin. Through its lessons and partnerships, the initiative shows that progress in groundwater governance is achievable and offers a practical model for other regions managing shared natural resources under increasing stress.

By Tom Sengalama, Team Leader, Nature, Climate, Environment and Resilience (NCER)