Though microplastic (MP/MiP) pollution of the environment is a popular research topic, a relatively limited number of studies are investigating its geomorphological context. However, site-specific hydrological and morphological parameters fundamentally affect the MP transport, deposition and mobilization. Therefore, we aimed to evaluate the geomorphological influencing factors on MP deposition in the fluvial sediments of the Tisza River (Central Europe). Between the two surveys (in 2019 and 2020), small flood waves rearranged the MP pollution, as in the sediments of the Tisza it decreased by 30% and in the tributaries by 48%. The previously highly polluted upstream and downstream sections became moderately polluted, but the contamination increased in the Middle Tisza, and the hot-spots were rearranged. The increasing longitudinal trend in the MP content exists if the minimum values of the hydrologically uniform sections are considered. The tributaries are important MP sources, as 80% of them had a higher (by 20%) MP content in their sediments than the Tisza had near the confluence, and they increased the MP content of the Tisza by 52% on average. The point-bars were the most polluted in-channel forms, while the side-bars and sediment sheets had less MP content, by 18 and 23%, respectively. The spatial trend of the MP content of these forms was not the same. Therefore, during the planning of sampling campaigns, it is very important to consider the geomorphological setting of a sampling site: we suggest sampling side-bars. No clear connection between the particle size of the sediments and their MP content was found.