Where should we take cores for palaeotsunami research? It is generally considered that local depressions with low energy environments such as wetlands are one of the best places. However, it is also recognized that the presence or absence of palaeotsunami deposits (and their relative thickness) is highly dependent upon subsoil microtopography. In the beach ridge system of Ishinomaki Plain, Japan, several palaeotsunami deposits linked to past Japan Trench earthquakes have been reported. However, the number of palaeotsunami deposits reported at individual sites varies considerably. This study used ground penetrating radar (GPR) combined with geological evidence to better understand the relationship between palaeotopography and palaeotsunami deposit characteristics. The subsurface topography of the ~3000–4000 bp beach ridge was reconstructed using GPR data coupled with core surveys of the underlying sediments. We noted that the number (and thickness) of the palaeotsunami deposits inferred from the cores was controlled by the palaeotopography. Namely, a larger number of events and thicker palaeotsunami deposits were observed in depressions in the subsurface microtopography. We noted a total of three palaeotsunami deposits dated to between 1700 and 3000 cal bp, but they were only observed together in 11% of the core sites. This result is important for tsunami risk assessments that use the sedimentary evidence of past events because we may well be underestimating the number of tsunamis that have occurred. We suggest that GPR is an efficient and invaluable tool to help researchers identify the most appropriate places to carry out geological fieldwork in order to provide a more comprehensive understanding of past tsunami activity. Copyright © 2017 John Wiley & Sons, Ltd.