Salinity is one of the most important abiotic stress factors that affect plant growth and limit agricultural productivity. In this study, the effects of iron (FeNP), silver (AgNP), and silicon dioxide (SiNP) nanoparticles on the morphological and physiological parameters of in vitro boysenberry plants grown under salinity stress (NaCl) were investigated. According to our study results, higher values were obtained from SiNP application in terms of shoot development parameters; FeNP application was found to be more successful for root development; AgNP application was effective in terms of SPAD, leaf relative water content (LRWC), and relative growth rate (RGR); and FeNP application increased superoxide dismutase (SOD) and catalase (CAT) enzyme activities. Salt stress significantly affected root development, SPAD values, LRWC and RGR, and SOD and CAT enzyme activities. As a result, under salt stress conditions, SiNP, FeNP, and AgNP applications can significantly reduce the negative effects of stress and promote the vegetative development of the plant compared to control conditions.