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Rock pools on granite outcrops occur worldwide and are poorly studied, despite their intrinsic biological interest. In semi-arid Botswana, such habitats occur mainly on the granite outcrops in the southwestern Hardveld zone. To date, studies on these systems have focused mainly on individual species or particular interactions. By means of frequent sampling (every other day) during an entire wet phase (hydrocycle), we attempted to get a time integrated overview of invertebrate species composition in a set of 18 rock pools from two clusters (meta-communities). A faunal list is presented and described. Rock pool species were separated in permanent and ephemeral inhabitants, based on their strategy to survive or escape the frequent dry phases of their habitat, respectively. A new chydorid species, four new turbellarian taxa and two new ostracod species were discovered. All new taxa were permanent inhabitants, illustrating the need for more intense and time-integrated studies of these ephemeral systems and especially the permanent residents with specific adaptations to the vagaries of their variable habitat. The best sampling strategy to assess species richness in these rock pool systems is to randomly sample three to four pools in a cluster, each in the final phase of their hydrocycle.