Disastrous floods in the twin cities of Nogales, Arizona, USA, and Nogales, Sonora, Mexico (collectively referred to as Ambos Nogales) occur annually in response to monsoonal summer rains. Flood-related hazards include property damage, impairment to sewage systems, sewage discharge, water contamination, erosion, and loss of life. Flood risk, particularly in Nogales, Sonora, is amplified by informal, “squatter” settlements in the watershed floodplain and associated development and infrastructure. The expected increase in precipitation intensity, resulting from climate change, poses further risk to flooding therein. We explore binational community perceptions of flooding, preferences for watershed management, and potential actions to address flooding and increase socio-ecological resilience in Ambos Nogales using standardized questionnaires and interviews to collect data about people and their preferences. We conducted 25 semi-structured interviews with local subject matter experts and gathered survey responses from community members in Ambos Nogales. Though survey response was limited, expected frequencies were high enough to conduct Chi-squared tests of independence to test for statistically significant relationships between survey variables. Results showed that respondents with previous experience with flooding corresponded with their level of concern about future floods. Additionally, respondents perceived greater flood-related risks from traveling across town and damage to vehicles than from inundation or damages to their homes or neighborhoods. Binationally, women respondents felt less prepared for future floods than men. On both sides of the border, community members and local experts agreed that Ambos Nogales lacks adequate preparation for future floods. To increase preparedness, they recommended flood risk education and awareness campaigns, implementation of green infrastructure, additional stormwater infrastructure (such as drainage systems), enhanced flood early warning systems, and reduction of flood flows through regulations to reduce the expansion of hard surfaces. This study contributes systematic collection of information about flood risk perceptions across an international border, including novel data regarding risks related to climate change and gender-based assessments of flood risk. Our finding of commonalities across both border communities, in perceptions of flood risk and in the types of risk reduction solutions recommended by community members, provides clear directions for flood risk education, outreach, and preparedness, as well as measures to enhance cross-border cooperation.