In this study, polyamide 66 (PA) and polyacrylonitrile (PAN) were electrospun with various arrangements on substrate surface. Spunbond-Meltblown-Spunbond polypropylene nonwoven (SMS) and carbon foam were applied as substrate to evaluate how filtration efficiency and flux is affected. In addition to substrate, the influence of polymer concentration and layer arrangement were studied. Taghuchi design was utilized for optimum structure recognition. A vat dye was used to study the filtration efficiency. The results have revealed that substrate type plays as the most effective factor among all parameters. SMS substrate was led to finer fibers fabrication, smaller pores, and therefore, superior filtration efficiency and higher flux. Although layer arrangement showed less impression than substrate, it was more effective than polymer concentration. Furthermore study on the base of Taghuchi design showed that by applying PAN/PA/PAN composite nanofibrous membrane on SMS substrate, a high filtration efficiency can be achieved by reduction of 99.58 and 86.13% turbidity and chemical oxygen demand, respectively.