Due to the scarcity of fresh water for crop irrigation in semi-arid areas, sustainable use of treated municipal wastewater is essential. Chlorine for wastewater disinfection added in wastewater treatment plants may be toxic for crops and can degrade cultivated soils. This study evaluates the crop and soil response to irrigation with treated municipal wastewater (with or without chlorination) in comparison to clear water. Small plants of tomato and cabbage and young bergamot trees were irrigated in pots throughout two months. The use of chlorinated or non-chlorinated wastewater did not significantly change biomass growth, morphological parameters and the efficiency of energy transfer. Significant reductions (40–50%) in the stem diameter of tomato and bergamot plants and differences (−25% to 53%) in all physiological parameters were measured for tomato immediately after the irrigation start. A decrease (−55%) in stomatal conductance and transpiration rate together with an increase (+80%) in water use efficiency were also recorded in bergamot after 30 days of irrigation. This type of irrigation water did not induce significant changes in soil properties, except for a decrease in pH (−20%) in bergamot soils after the irrigation start and in electric conductivity (EC, −40%) at the end of the irrigation period for all species. Irrigation of plants with chlorinated wastewater increased the weight of the fresh biomass (+56%) of leaves and the stem diameter (−60%) of tomato and decreased water use efficiency (+67%) in bergamot after the irrigation start. After two months, decreases in stomatal conductance and transpiration rate in cabbage (over 50%) and increases in water use efficiency in cabbage and bergamot (by 40% and 70%, respectively) were evident. Among the studied soil properties, land application of chlorinated wastewater only reduced electrical conductivity (−47%). Overall, this study demonstrated that the use of treated municipal wastewater (with or without chlorination) does not have detrimental impacts on both plant growth (at least for tomato, cabbage and bergamot) and soil health in the short term.