Heat has been widely applied to trace groundwater‐surface water exchanges in inland environments, but it is infrequently applied in coastal sediment where head oscillations induce periodicity in water flux magnitude/direction and heat advection. This complicates interpretation of temperatures to estimate water fluxes. We investigate the convolution of thermal and hydraulic signals to assess the viability of using heat as a tracer in environments with tidal head oscillations superimposed on submarine groundwater discharge. We first generate sediment temperature and head time series for conditions ranging from no tide to mega‐tidal using a numerical model (SUTRA) forced with periodic temperature and tidal head signals. We then analyze these synthetic temperature time series using heat tracing software (VFLUX2 and 1DTempPro) to evaluate if conventional terrestrial approaches to infer fluxes from temperatures are applicable for coastal settings. We consider high‐frequency water flux variability within a tidal signal and averaged over tidal signals. Results show that VFLUX2 analytical methods reasonably estimated the mean discharge fluxes in most cases but could not reproduce the flux variability within tidal cycles. The model results further reveal that high‐frequency time series of water fluxes varying in magnitude and direction can be accurately estimated if paired temperature and hydraulic head are analyzed using numerical models (e.g. 1DTempPro) that consider both dynamic hydraulic gradients and thermal signals. These results point to the opportunity to incorporate pressure sensors within heat tracing instrumentation to better assess sub‐daily flux oscillations and associated reactive processes.