The surface morphology and deuterium retention were investigated of polycrystalline tungsten targets that were exposed to deuterium plasmas at widely varying conditions. By changing only one parameter at a time, the isolated effects of flux, time and pre-damaging on surface modifications and deuterium retention were studied. The sample exposed to low-flux plasma (1020 m−2s−1) is mostly smooth with only a few areas containing very large blisters (50–500 µm). The samples exposed to high-flux plasmas (1024 m−2s−1) show large numbers of smaller blisters (1–10 µm) and in addition even smaller protrusions (<750 nm). The size of the blisters and their density strongly increase with fluence. Pre-damaging tungsten with MeV ions leads to less blisters but to more protrusions. In addition to these (sub-)micrometer-sized structures, all samples show formation of nanostructures. Comparison of a low-flux and high-flux sample exposed to similar fluence showed that the variation in morphology is dominated by the flux differences. It is shown that the blisters and protrusions originate in inter- and intra-granular cavities, respectively. The depth of the cavities underneath the surface correlates well with the depth distributions of the retained deuterium. Trapping of significant amounts of deuterium therefore seems to take place in and/or close to these cavities and gives rise to an additional peak in the thermal desorption spectrum at 700 K.