Hawaiian fishponds, or loko i‘a, are ancient aquaculture systems and models of sustainable aquatic resource management from traditional Native Hawaiian harvest practices. Of the 488 fishponds documented in ancient Hawai‘i, only 38 are currently actively managed. Building on Indigenous and local knowledge, fishponds are being adapted to current community needs. Functional fishponds perpetuate culture, improve food security, enhance ecosystem services and transform conservation biology through Indigenous perspectives. Here we examine how Indigenous practices effectively maintain sustainable harvest of an introduced, but economically important, crab species, the mud crab, Scylla serrata (Forskål 1775). The State of Hawai‘i has only a size limit, and no bag limits, for this species. With Indigenous management in a Hawaiian fishpond, limits are set and enforced in response to fluctuations in catch. We used a mark–recapture experiment to parameterise a size-structured population model, which we used to investigate the impact of changing harvest rates. Throughout the study period of 2017–20, the mean number of crabs per harvest was 28 individuals (s.d. = 7) and average catch per unit effort was 0.20 crabs per trap-hour (s.d. = 0.054). During winter, catch per unit effort was lower but mean crab size was larger than during summer. Model simulations indicated that current Indigenous practices are less likely to cause a decline in population growth rate than a strict size limit. Using information from Indigenous harvest practices and the mark–recapture study, we codeveloped a versatile crab population model that can be tailored to changing management objectives.