Innovation processes face significant and not well-understood uncertainties in resource-constrained environments in developing countries. Through a case study of a water innovation process focused on Kenya, this article studies the prevailing uncertainties and management principles. With the help of a framework that combines information on technological, organizational, commercial and social aspects, our study identifies uncertainties in four distinctive stages of resource-constrained innovation: (1) Ideation and conceptualization, (2) Learning-based product and business development, (3) Scrutinized product and business development and (4) Commercialization. We recognize three principles required to manage uncertainties and develop successful resource-constrained innovations: (1) the utilization of versatile research and development approaches, (2) building internal acceptability, trust and legitimacy and (3) leveraging range of partnerships and networks to access complementary resources and capabilities in different process stages. Our findings suggest that management of uncertainties requires proactive utilization of partner networks and context-specific strategies in different stages. With this research, we contribute to the understanding of innovation processes by advancing process-based knowledge of water innovation, uncertainties and related management strategies in resource-constrained environments.