We investigated the effects of root-zone environment, humidity around the roots and nutrient solution on the activity and morphology of tomato roots grown in wet-sheet culture (exposed to air) or deep flow technique (submerged in solution). Differences in root external and internal structure between treatment groups could be interpreted as adaptive responses to the root environment. The exposed roots could adapt more readily to extremes of temperature than those in the solution. Those adaptations occurred through short-term physiological responses and long-term additive morphological responses. We also evaluated the facilitating effects of the flow of nutrient solution on root respiration and nutrient uptake rate. Where the root system was split between humid air and nutrient solution, roots in the solution absorbed and supplied nitrogen more efficiently per dry weight than did roots in air. Split root systems between humid air and nutrient solution showed stable growth of tomato plants. Our observations of root plasticity will help the establishment of growing systems that support high yield and stable production.