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Lutraria rhynchaena Jonas, 1844 is of great commercial interest, but its reserves have dramatically declined over recent decades. Therefore, there is an urgent need of scientific basis to propose effective fishery management measures and improve artificial aquaculture of the clam. In this study, we investigated the distribution and density of L. rhynchaena, sediment characteristics, and established the clam’s reproductive cycle through monthly observations from August 2017 to July 2018. The study results showed that distribution and density of clams are related to sediment types, and the sediment type of medium sand is likely the best benthic substrate for the clams. The spawning of clams occurred throughout the year with three spawning peaks in January, April and September. For the sustainable management of the clam resource in Cat Ba-Ha Long Bay, the fishery authorities can issue a ban on harvest of the clam in spawning peak months in January, April and September.