Hydroponic cultivation using organic, fully biodegradable substrates that provide the right physical properties for plant growth and development is now the future of soilless production. Despite the high productivity and strict control of production conditions in this method, excessive salinity of the substrate often occurs. However, recent research results indicate that salinity at a high enough threshold can improve yield quality, while prolonged exposure to too high EC, or exceeding the safe EC threshold for a given species, leads to reduced quality and reduced or even no yield. The aim of this study was to determine the effect of biodegradable lignite substrate (L) and eustressor in the form of high EC nutrient solution (7.0 dS·m−1) on morphological and physiological parameters, as well as the quality and yield of cucumber (Cucumis sativus L.) in hydroponic cultivation compared to the mineral wool substrate (MW). The MW/high EC combination showed a significant reduction in shoot diameter by nearly 6% compared to the MW/control EC combination. The stomatal conductance (gs) and the transpiration rate (E) were also significantly reduced in this combination. The present study indicates that the effects of eustressor application vary depending on the growing medium used, and more favorable effects in terms of yield quality were obtained using biodegradable lignite substrate. The high EC of nutrient solution combined with lignite substrate (L/high EC) significantly increased in cucumber fruit the content of β-carotene, lutein, chlorophyll a, chlorophyll b and the sum of chlorophyll a + b by 33.3%, 40%, 28.6%, 26.3% and 26.7%, respectively, as compared to MW/high EC combination.