Abstract Decapods associated with two species of seagrass (Zostera capricorni and Posidonia australis) were sampled at several sites within estuaries on the New South Wales coast for 3 years. Two species of decapod (Macrobrachium intermedium and Penaeus plebejus) were abundant in Z. capricorni. Four species (M. intermedium, P. plebejus, Chlorotocella leptorhynchus and Nectocarcinus tuberculosus) were abundant in P. australis. Abundance of all these species fluctuated greatly among sites and through time. Some seasonal patterns in abundance were evident, and appeared to be caused by recruitment and subsequent mortality or migration of individuals. Similarly, there were some consistent spatial patterns in abundance of most species. In particular, some sites supported consistently more juveniles during the same period of separate years. Within Jervis Bay, P. australis was also sampled in shallow (1–2m) and deep (7–8 m) water. Three species were abundant (C. leptorhynchus, N. tuberculosus and Processa australiense), but showed no consistent differences between the two depths. Abundances of these species did fluctuate greatly among the sites within Jervis Bay and through time. Such observations of the natural rates of change in abundance of populations are essential in order to be able to detect the effects of human disturbances.