The source characteristics of offshore seismic events, especially regular (or fast) and slow earthquakes, can provide key information on their source physics and frictional conditions at the plate boundary. Due to strong 3-D heterogeneities in offshore regions, such as those relating to sea water, accretionary prism and small-scale velocity heterogeneity, conventional methods using a 1-D earth model may mis-estimate source parameters such as the duration and radiation energy. Estimations could become severe inaccuracies for small offshore seismic events because high-frequency (>1 Hz) seismograms, which are strongly affected by 3-D heterogeneities, are only available for analysis because of their signal-to-noise ratio. To investigate the effects of offshore heterogeneities on source parameter estimation for small seismic events, we analysed both observed and simulated high-frequency seismograms southeast off the Kii Peninsula, Japan, in the Nankai subduction zone. Numerical simulations of seismic wave propagation using a 3-D velocity structure model clarified the effects of each heterogeneity. Comparisons between observations and model simulations demonstrated that the thick low-velocity accretionary prism has significant effects on high-frequency seismic wave propagation. Especially for shallow low-frequency tremors occurring at depths just below the accretionary prism toe, seismogram durations are significantly broader than an assumed source duration, even for stations with epicentral distances of approximately 10 km. Spindle-shape seismogram envelopes were observed even at such close stations. Our results suggest that incorporating 3-D heterogeneities is necessary for practical estimation of source parameters for small offshore events.