A characterization of hyporheic exchange for dry and wet season baseflow, as well as partially dewatered discharge, was done in Prieta Creek, a first-order cascade in northern Honduras. The cascade had discharges from 1 to 15 l s−1, had average slopes of 12%, pool spacing of 3 m, and shallow substrate of sand and gravel. Tracer tests were conducted in a 15-m sub-reach, a length considered to be adequate for the experiment based on the DaI test, a ratio of exchange and transport processes. In the three tests, between 9 and 18% of tracer was not recovered, possibly due to entrainment in flowpaths passing beneath the downstream monitoring location. Tracer data were analysed by the one-dimensional transport with inflow and storage (OTIS) transient storage model (TSM) to derive standard exchange parameters, and by the solute transport in rivers (STIR) model to examine hyporheic residence time distributions (RTDs). The best fit of the observed tracer breakthrough curves was obtained by using the STIR model with a combination of two exponential RTDs to represent hyporheic retention. With increasing discharge, the OTIS model predicted increasing storage exchange fluxes and exchange coefficients and decreasing storage zone areas and transient storage times, which are trends supported by riparian and streambed piezometric head data. Riparian water levels rose during the transition from the dry to wet season, which could constrict the hyporheic storage zone. Thirteen of the 19 streambed piezometers recorded seasonal changes in hydraulic gradients and flux direction, with fewer yet stronger upwelling zones during higher discharges. The MODFLOW model missed the observed seasonal changes, possibly due to subtle changes in the seasonal change in water surface profiles. We conclude that partially dewatered dry season exchange, compared to wet season exchange, was initiated and terminated with smaller pressure gradients and, in different streambed locations, was smaller in volume, had longer residence times, and may connect with deeper and longer flow paths. Copyright © 2010 John Wiley & Sons, Ltd.