It is difficult to obtain reliable heat flow values in shallow sea areas where the bottom water temperature is not stable. We attempted to measure heat flow in shallow seas by monitoring temperature profiles in sediments, using pop-up type instruments with 2 m long temperature probes. Long-term temperature records for over 200 days were obtained at four stations off southwest Japan. Analysis of the data showed the bottom water temperature variations (BTV) were propagated through sediments by thermal diffusion only. We could then remove the influence of BTV from the temperature records and determine the heat flow, though the effect of longer period components in BTV has possibly remained. The obtained heat flow values are consistent with those estimated from depths of gas hydrate BSRs in the vicinities of the stations. These results indicate that long-term temperature monitoring is a useful method for heat flow determination in shallow seas.