This sub-collection is the result of an investigation into the mechanism of organic fouling in membrane filtration processes. In this experiment, poly(vinylidene fluoride) (PVDF) membranes were used to filter three types of organic foulants, yeast, protein and sodium alginate with a concentration of 50mg/l, 40mg/l and 20 mg/l, respectively, from suspension in a dead-end filtration cell. These model foulants were stained with fluorescent dyes before filtration. This dataset contains a stack of images of the fouling layer on the PVDF membrane surface captured by a confocal laser scanning microscope (CLSM) and its associated acquisition software. This dataset would be useful to researchers who are investigating the membrane organic fouling mechanism so that new membrane materials and new anti-fouling surface treatment technologies can be developed for water and wastewater industry in the future .