Aims <p>Soil salinity and nitrogen (N) distribution are often heterogeneous in the soil. However, the combined effects of salinity and N heterogeneity on plant water use efficiency (WUE) and fruit quality remain poorly understood.</p> Methods <p>A split-root pot experiment was conducted with three salinity distributions, viz. S_1:5 (1‰/5‰ by mass of soil in side-A/side-B), S_2:4 (2‰/4‰) and S_3:3 (3‰/3‰), combined with three N application patterns, including N_4:0 (270/0&#xa0;mg&#xa0;kg⁻¹ by mass of soil in side-A/side-B), N_0:4 (0/270) and N_2:2 (135/135).</p> Results <p>Compared with S_3:3, non-uniform salinity (S_1:5 and S_2:4) combined with local N supply at high-salinity side (N_0:4) enhanced the intrinsic WUE (WUE_i, A_n/g_s) and whole-plant WUE (WUE_p, total dry biomass/ water use), due to reduced g_s from flowering to ripening stage. Visual and storage fruit-quality traits, including fruit firmness and shape index were significantly enhanced by N_0:4 compared to N_2:2 and N_4:0, while fruit water content was reduced. Fruit firmness increased with reduced fruit water content and a lower root dry matter ratio between side-A and side-B. Moreover, fruit Δ¹³C were significantly decreased by N_0:4 compared to N_2:2 and N_4:0. Among all organs, fruit Δ¹³C was most strongly correlated with whole-plant Δ¹³C and WUE_p, but unrelated to visual and storage traits.</p> Conclusions <p>Localized N application in high-salinity zone enhanced water productivity and fruit visual and storage quality, offering a strategy to improve tomato performance under saline conditions. Furthermore, fruit Δ¹³C is suggested as a reliable organ-specific indicator of whole-plant water status under heterogeneous salt and N conditions.</p>