This study describes the development of WACCShed, an agent-based software platform that permits the systematic study of interactions among hydrology, climate, and strategic human decision-making in a watershed over time. To illustrate the capabilities of the platform, findings are reported for a base-case application reflecting, in simplified form, the structural attributes of the Squaw Creek watershed in central Iowa. Attention is focused on the alignment of welfare outcomes as a prerequisite for effective watershed governance. Key treatment factors include farmer and city manager decision modes for land and budget allocations, farmer targeted savings, and the effectiveness of city levee investments for the mitigation of city flood damage. Welfare misalignment is found to arise across a broad spectrum of settings for these treatment factors.