Extreme weather events including flooding can have severe personal, infrastructural, and economic consequences, with recent evidence pointing to surface flooding as a pathway for the microbial contamination of private groundwater supplies. There is a pressing need for increasingly focused information and awareness campaigns to highlight the risks posed by extreme weather events and appropriate subsequent post-event actions. To date, little is known about the presence, directionality or magnitude of gender-related differences regarding flood risk awareness and behaviour among private groundwater users, a particularly susceptible sub-population due to an overarching paucity of infrastructural regulation across many regions. The current study investigated gender-related differences in flood risk perception and associated mitigation behaviours via a cross-sectional, national survey of 405 (168 female, 237 male) private groundwater supply users. The developed survey instrument assessed socio-demographic profile, previous flood experience, experiential and conjectural health behaviours (contingent on previous experience), and Risk, Attitude, Norms, Ability, Self-regulation (RANAS) framework questions. Statistically significant gender differences were found between both ‘Norm—Descriptive’ and ‘Ability—Self-efficacy’ RANAS elements (p < 0.05). Female respondents reported a lower level of awareness of the need for post-flood action(s) (8.9% vs. 16.5%), alongside a perceived “lack of information” as a reason for not testing their domestic well (4.9% vs. 11.5%). Conversely, male respondents were more likely to report awareness of their well location in relation to possible contamination sources (96.6% vs. 89.9%) and awareness of previous water testing results (98.9% vs. 93.0%). Gender-related gaps exist within the studied private groundwater reliant cohort, a sub-population which has to date remained under-studied within the context of climate change and extreme weather events. Accordingly, findings suggest that gender-focused communication and education may represent an effective tool for protecting current and future generations of global groundwater users.