Microplastics exhibit high spatial variation across the marine environment, this creates difficulties drawing conclusions and making inferences from data. Robust monitoring programs allow us to make informed management decisions on the regulation of microplastic pollution. global monitoring practices for microplastics in marine environments were evaluated by a systematic review and was used to inform the design of a monitoring program that best represents the high spatial variability of microplastics between sites. Based on common monitoring practices, a pilot study across four sites (n = 9 samples per site) in western Port Phillip Bay estimated the levels of background variation to determine the appropriate levels of replication for the primary sampling. The pilot study indicated high levels of spatial variation between and within sites. At two sites the standard deviation was close to the average (185.71 ± 172.24 at Geelong, and 776 ± 578 at Indented Heads), and at one site the standard deviation was greater than the average (321.33 ± 437.72). Power calculations suggest 30 to 40 samples per beach to detect changes in microplastic abundance across sites. This process is to be condensed into a decision tool for regulators and researchers to facilitate the design of microplastic monitoring programs.