Efforts were undertaken through the auspices of a collaborative project “Strengthening Universities Capacities for Mitigating Climate Induced Change Water Vulnerability – WATERCAP” to address a key challenge of water scarcity in dryland areas of Uganda. A multisciplinary team engaged since 2009 has through implementation of this project observed the constraints and opportunities that impede and or enhance functional partnership in an inter and multi-disciplinary projects aimed at enhancing agricultural and community development. Nonetheless, functional partnerships create networks and sustainable innovation platforms that open opportunities for joint research and learning, community involvement and dissemination of new technologies, knowledge and innovation to the endusers. Sustainable partnerships also provide space for mentorship opportunities and bring together different partners with unique mandates and values to address real life problems. However, seemingly functional partnerships can also be constrained by failure to appreciate mandates and value alignment of different partners and failure to pursue a common goal among the actors. Partnerships are further constrained by poor communication and reporting skills of project outcomes as well as inequity in the sharing of project resources and ownership of project outcomes. Understanding the constraints and opportunities of partnerships between universities and development agencies enabled the WATERCAP project to find appropriate entry points to support the innovation platforms for enhancing the resilience of smallholder farmers to climate change induced water vulnerability.