In African small-scale agriculture, sustainable land and water management (SLWM) is key to improving food production while coping with climate change. However, the rate of SLWM adoption remains low, suggesting a gap between generalized SLWM advantages for rural development across the literature, and the existence of context-dependent barriers to its effective implementation. Uganda is an example of this paradox: the SLWM adoption rate is low despite favorable ecological conditions for agriculture development and a large rural population. A systemic understanding of the barriers hindering the adoption of SLWM is therefore crucial to developing coherent policy interventions and enabling effective funding strategies. Here, we propose a cross-scale archetype approach to identify and link barriers to SLWM adoption in Uganda. We performed 80 interviews across the country to build cognitive archetypes, harvesting stakeholders’ perceptions of different types of barriers. We complemented this bottom-up perspective with a spatial archetype analysis to contextualize these results across different social-ecological regions. We found poverty trap, overpopulation, risk aversion, remoteness, and post-conflict patriarchal systems as cognitive archetypes that synthesize the different dynamics of barriers to SLWM adoption in Uganda. Our results reveal both specific and cross-cutting barriers. Ineffective extension services emerges as a ubiquitous barrier, whereas gender inequality is a priority barrier for large supported farms and farms in drier lowlands in northern Uganda. The combination of cognitive and spatial archetypes proposed here can help to overcome ineffective “one-size-fits-all” solutions and support context-specific policy plans to scale up SLWM, rationing resources to support sustainable intensification of agriculture.