Background Salinity is one of the most lethal abiotic stresses which affect multiple aspects of plant physiology. Natural variations in plant germplasm are a great resource that could be exploited for improvement in salt tolerance. Eruca sativa (E. sativa) exhibits tolerance to abiotic stresses. However, thorough evaluation of its salt stress tolerance and screening for traits that could be reliably applied for salt tolerance needs to be studied. The current study was designed to characterize 25 E. sativa accessions, originating from diverse geographical regions of Pakistan, for the salt stress tolerance. Methods Salt stress (150 mM NaCl) was applied for 2 weeks to the plants at four leaf stage in hydroponics. Data of the following morpho-physiological traits were collected from control and treated plants of all the accessions: root length (RL), shoot length (SL), plant height (PH), leaf number (LN), leaf area (LA), fresh weight (FW), dry weight (DW), chlorophyl content (SPAD), electrolyte leakage (EL), relative water content (RWC), gas exchange parameters and mineral ion content. Salt tolerance was determined based on membership function value (MFV) of the tested traits. Results Compared with control, the salt-stressed group had significantly reduced mean SL, RL, PH, LN, LA, FW, DW and SPAD. NaCl treatment triggered a slight increase in EL in few accessions. Mean RWC of control and treated groups were not significantly different although few accessions exhibited variation in this trait. Salt stress caused a significant reduction in photosynthesis rate (PR), transpiration rate (TR) and stomatal conductance (SC) but intercellular CO2 (Ci) was not significantly different between control and treated groups. Compared with control, the salt-stressed plants accumulated significantly higher Na+, K+ and Ca2+ while significantly lower Mg2+. K+/Na+ ratio was significantly decreased in salt-stressed plants compared with control. Importantly, significant inter-accession variations were found for all the tested traits. The principal component analysis identified SL, RL, PH, LN, LA, FW, DW and PR as the most significant traits for resolving inter-accession variability. Based on MFV of the tested traits, accessions were categorized into five standard groups. Among 25 accessions, one accession was ranked as highly tolerant, four as tolerant while 15 accessions were ranked as moderately tolerant. Of the remaining five accessions, four were ranked as sensitive while one accession as highly sensitive. Conclusion E. sativa accessions were found to exhibit significant genetic diversity in all the tested traits. A few most significant traits for dissecting the genetic variability were identified that could be used for future large-scale germplasm screening in E. sativa. Salt tolerant accessions could be a good resource for future breeding programs aiming to improve salt stress tolerance.