In Tokyo Bay, the harvestable quantity of asari (Manila) clams Ruditapes philippinarum has been decreasing since the late 1990s. We conducted a field investigation on clam density in the Banzu culture area from April 1988 to December 2014 and collected records spanning January 1986 to September 2017 from relevant fisheries cooperative associations to clarify the relationship between the temporal variation in stock abundance and the production activities of fishermen. The yearly variation in clam abundance over the study period was marked by larger decreases in the numbers of larger clams. A large quantity of juvenile clams, beyond the biological productivity of the culture area, may have been introduced as seed stock in the late 1980s despite the high level of harvestable stock. The declines in harvested quantity began in the late 1990s and may have been caused by decreases in harvestable stock despite the continuous addition of seed stock clams. The harvested quantity is likely to be significantly dependent upon the wild clam population, even within the culture area, as the harvestable quantity was not correlated with the quantity of seed stock introduced during the study period. These declines in harvested quantity may have resulted from a decreasing number of operating harvesters due to the low level of harvestable stock and consequently reduced profitability. Two findings were emphasized. A certain management style, based on predictions of the contributions of wild and introduced clams to future stock biomass, is essential for economically-feasible culturing. In areas with less harvestable stock, actions should be taken to maintain the incomes of harvesters while avoiding overexploitation, even if the total harvest quantity decreases.