Water convolvulus is an aquatic plant capable of growing in a low nutrient solution and poor water quality. There are many reports on utilization of this plant for the efficient remediation of salt contaminated wastewater. The aim of this investigation was to identify the criteria that could be used to classify the salt tolerance and salt sensitivity of water convolvulus using multivariate characters. Six lines of water convolvulus plantlets were photoautotrophically grown in a controlled environmental system and then treated with 0 (control) or 342 mM NaCl (salt stress) for a week. Pigment levels, chlorophyll a fluorescence and growth reduction were measured as potential multivariate parameters to group plants into two classes: salt tolerant (WC083, SR739 and SR716) and salt sensitive (MK98, WC001 and WC092). Total chlorophyll and carotenoid pigments in salt-stressed plantlets were reduced by 80.0% and 68.6% in salt tolerant lines. In salt-sensitive lines these pigments were degraded by 88.0% and 79.8%, respectively. This suggests that the major pigments, total chlorophyll and carotenoids in salt-tolerant lines were more stable than those in salt-sensitive lines. The function of both major pigments in salt-tolerant lines was strongly related to light harvesting (ΦPSII) (r = 0.81) and photooxidative damage (NPQ) defenses (r = 0.81), respectively. Further, several growth parameters (plant height, number of leaves, root length, number of roots, fresh weight) progressively decreased when exposed to salt stress, especially in salt-sensitive lines. The salt-tolerant lines of water convolvulus can be further utilized for NaCl-contaminated wastewater phytoremediation, while the salt-sensitive lines may be applied as effective indicators of salt contamination in the water.