We analyse archaeobotanical remains from three excavated rockshelter sites, Jinmium, Granilpi and Punipunil, in the Keep River region, northwestern Australia. The record is dominated by burnt fragmented seed remains from the fruit trees Persoonia falcata and Buchanania obovata, consistent with ethnographic records of whole fruits being pounded into pastes and cakes at the beginning of the summer wet season. Surface seed samples of non-cultural origin are mostly whole and unburnt, and contain higher proportions of grass seeds. Sustained processing of fruit seeds is first visible in the archaeological record about 3500 years ago. Spatial and temporal variation in its intensity is evident since that time until it declines following European colonisation. The decline does not represent total site abandonment, but a reorientation of activities following the ecological and social changes that came with pastoralism. The former included the local decline of P. falcata with more intense fire regimes.