Improving rural water supply sustainability in sub-Saharan Africa remains a major challenge. This study analysed five-years of cross-sectional sustainability check data collected annually between 2011 and 2016 (except 2015) to investigate factors influencing the operational performance of community-managed handpumps in rural Mozambique. Logistic and negative binomial regression was performed using multiple outcome measures of functionality, reliability and continuity. Average marginal effects (AMEs) were estimated to assess the effects of the predictors and mediation analysis was conducted to examine the role of women's participation.Higher levels of handpump performance were associated with financial records quality and update frequency, water committees with spare parts in stock, and committee annual revenue. The AME of high quality or recently updated financial records for non-functionality was estimated to be −0.40 (95% confidence interval [CI], −0.56 to −0.25), which is interpreted as a 40% lower probability of a water point being non-functional compared to the reference group. Water committees with a spare part stock exhibited a preventive effect on both non-functionality and breakdowns in the past 12 months, reducing their probability by 10% (AME, 95% CI, −0.17 to −0.03) and by 18% (AME, 95% CI, −0.30 to −0.05), respectively. Annual committee revenue up to 2,000 MZN (57 USD) reduced the probability of breakdowns by 25% (AME, 95% CI, −0.45 to 0.05). Handpumps were 10% (AME, 95% CI, 0.03 to 0.17) more likely to be non-functional when women were in the committee management positions. Conversely, female maintenance group members were associated with reduced breakdowns in the multivariate regression analysis (odds ratio, 0.48; 95% CI, 0.24 to 0.95).Increasing outreach of post-construction support on capacity building for water committees, particularly on user fee collection, maintaining financial records, replenishing spare parts, and increased participation of women in the maintenance group, may contribute to greater sustainability of rural water points.