The aim of this study was to determine the size distribution and flux of the mineral fraction collected in marine sediment traps in Mejillones Bay (23° S) using image-based size analysis. In this bay the material settling in the water column is a mixture of biogenic particles and lithic grains. The sediments analyzed correspond to four samples collected in the austral spring of 2008. We used image-based size analysis because it presents several advantages, which makes it an ideal method to study fine marine sediments. This analysis also yielded important information about the aspect and the morphology of the particles. In order to analyze the lithic fraction only, different pretreatments were applied and size—analyses were carried out with and without image information. Besides the main lithic components (quartz, feldspar, amphiboles, and micas), some nonlithic particles corresponding mainly to organic-matter remains were observed in the images, showing that the pretreatment was not fully effective. Biogenic silica and unexpected dark particles of probable anthropogenic origin were also detected. To avoid the influence of nonlithic grains in the analysis, the images were filtered based on the aspect of the particles using various discrimination tools. Before and after this removal, the size distributions of the samples were estimated and used to calculate the total flux. As compared to the flux of lithic particles, this total flux displays a systematic overestimation of up to 12%. As a consequence, using image-based size analysis allows not only enhancing the determination of the size distribution and flux but also controlling and improving the pretreatments protocols.