Seafloor litter is the least exploited component of marine litter. The spatially variable distribution of their densities over time is a cumulative effect of sources’ intensities and natural drivers like wind/wave and current conditions in interaction with seafloor morphology. Making safe interpretations about the exact spatiotemporal distribution of benthic litter requires good knowledge of the local above-mentioned seafloor components. In this work, visual monitoring over 3 years of a shallow urbanized bay in Syros Island, Cyclades, Greece, was proved a reliable way to assess the intensity of litter sources along their coasts. It showcased that spatial ranges that are influenced mainly by the annual ocean dynamics should be treated with caution or even excluded from the analysis. There, intense litter fluxes over the year, hinder any effort to separate local anthropogenic littering intensity changes from natural litter input-output fluctuations. Towed underwater camera surveying and auxiliary bathymetric and swath sonar backscatter datasets were used to find links between the seafloor litter transport dynamics and the seabed micro- and macro-topography, finally indicating litter traps and sinks.