The citrus yield is limited by soil and/or water salinity, but appropriate rootstocks can ensure the sustainability of the production system. Therefore, the objective of the present research was to evaluate the salt content in the soil and the production and physiological aspects of the ‘Tahiti’ acid lime combined with thirteen rootstocks, irrigated with saline water in the first two production years to identify indicators of salt tolerance. The rootstocks evaluated were: ‘Santa Cruz Rangpur’ lime, ‘Indio’, ‘Riverside’ and ‘San Diego’ citrandarins, ‘Sunki Tropical’ mandarin, and eight hybrids, obtained from the Citrus Breeding Program of Embrapa Cassava and Fruits. The waters used had three saline levels: 0.14, 2.40, and 4.80 dS m−1, in a randomized block adopting a split-plot design, with rootstocks in the plots and saline waters in the subplots, with four replicates. From August 2019 to February 2021, fruit harvests and agronomic traits were measured. At the end of each production year, the soil characteristics, leaf gas exchange, and chlorophyll a fluorescence analysis were performed. It was concluded that: (1) the effects of water salinity on citrus are of osmotic nature, reducing gas exchange, (2) the salinity did not significantly damage the photosynthetic apparatus until the second year of production, and (3) using more stable, salt-tolerant rootstocks makes it possible to cultivate ‘Tahiti’ acid lime under irrigation with waters of 2.4 dS m−1 electrical conductivity.