Fishery managers rely on species information, such as abundance and biomass, to optimise harvest strategies and establish suitable total allowable commercial catch. In fisheries that lack data from commercial operators, fishery-independent data can underpin assessments and inform management decisions. However, field-sampling programs are costly and require appropriate design to avoid obtaining biased data. In Coffin Bay, SA, the 50 t Vongole Fishery (Katelysia spp.) contains four primary fishing grounds and uses fishery-independent surveys to determine harvestable biomass and exploitation rate (i.e. catches at or below 7.5% of biomass estimates). Recent budget constraints resulted in implementation of a triennial sub-sampling program whereby at least one primary fishing ground is sampled annually on a rotational basis with spot sampling occurring outside the main area (N=124–149 transects). Investigations of 2015 survey data, which reflect complete sampling of all fishing grounds (N=223), showed that the triennial sampling program biased exploitation rates by -1.4% to 19.8%. Furthermore, random selection of 25%, 50% and 75% of data resulted in high variation among biomass estimates for K. rhytiphora but not K. scalarina. By understanding the impacts of sampling programs on biomass estimates, survey designs can be optimised to produce the best possible biomass estimates within budget constraints.