Although environmental flow regime assessments are becoming increasingly holistic, they rarely provoke water managers to enact the adaptive water reallocation mechanisms required to secure environmental water for wetlands. The conditions that cause science-based environmental flow assessments to succeed or fail in informing the management of environmental water requirements remain unclear. To begin to resolve these conditions, we used process tracing to deconstruct the sequence of activities required to manage environmental water in four case studies of seasonally ponding wetlands in Mediterranean and Mesoamerican watersheds. We hypothesized that, when the flexibility and equitability of the socioeconomic system do not match the complexity of the biophysical system, this leads to a failure of managers to integrate scientific guidance in their allocation of environmental water. Diagnostic evidence gathered indicates that science-management partnerships are essential to align institutional flexibility and socioeconomic equitability with the system’s ecohydrological complexity, and thus move from determination to reallocation of environmental water. These results confirm that institutions e.g., river basin organizations need to be supplemented by motivated actors with experience and skill to negotiate allocation and adaptive management of environmental water. These institutional-actor synergies are likely to be especially important in water scarce regions when the need to accommodate extreme hydrological conditions is not met by national governance capacity. We conclude by focusing on benefit sharing as a means to better describe the conditions for successful science-based environmental flow assessments that realize productive efficiency in environmental water allocation i.e., recognition of multiple values for both people and ecosystems.