Water management and distribution rules in flood-based livelihood systems (FBLS) have a key role in enhancing system-wide productivity and livelihoods. While such potential has to a certain extent been harnessed in DG Khan FBLS in Pakistan, it has not yet been fulfilled in the Tana River and Fogera FBLS in Kenya and Ethiopia, respectively. These three systems are considered among the major sources of water and food security in their respective regions by the local governments and communities. Drawing from 105 individual interviews with Pakistani FBLS farmers, the paper establishes that a package of water management and distribution rules have significantly contributed to (a) mitigating excessive upstream floodwater use, (b) reducing downstream water scarcity and (c) realizing nearly 4 tons ha−1 harvest of the major wheat crop across the upstream and downstream areas. This yield is about 20% higher than the country-wide average, and two-third of the maximum achievable. Furthermore, 86% of the upstream and three in four of the downstream farmers have managed to cover their livelihood needs that included health, school, housing, transportation, energy and food expenses. On the other hand, the analyses based on individual interviews with 94 and 147 FBLS farmers from Kenya and Ethiopia respectively, uncovered the negative consequences of the absence of a comprehensive package of water management and distribution rules. In Kenya, the downstream small-scale farmers that account for two-third of the Tana River FBLS population frequently suffer from floodwater scarcity. They could not cultivate the high return rice crop and their staple maize yield was low at about 1.25 tons ha−1 or 20% of the maximum attainable. Four in five reported poor livelihoods. The upstream large-scale farmers however often diverted excessive floodwater; over 90% usually grow rice as well as maize as a second crop for home consumption. The situation in Fogera is similar. The water distribution rules prioritized the upstream rice cultivation introduced a decade back to boost economic growth. This, as informed by 95% of the interviewed farmers, has caused downstream floodwater scarcity, about 30% maize yield reduction and livelihood deterioration. These findings on the impacts of water distribution rules can contribute to formulating investments that better achieve the productivity and livelihood potentials of FBLS across Africa and globally.