With salt stress presenting a major threat to global food production, attention has turned to the identification and breeding of crop cultivars with improved salt tolerance. For instance, some accessions of wild species with higher salt tolerance than commercial varieties are being investigated for their potential to expand food production into marginal areas or to use brackish waters for irrigation. However, assessment of individual plant responses to salt stress in field trials is time-consuming, limiting, for example, longitudinal assessment of large numbers of plants. Developments in Unmanned Aerial Vehicle (UAV) sensing technologies provide a means for extensive, repeated and consistent phenotyping and have significant advantages over standard approaches. In this study, 199 accessions of the wild tomato species, Solanum pimpinellifolium, were evaluated through a field assessment of 600 control and 600 salt-treated plants. UAV imagery was used to: (1) delineate tomato plants from a time-series of eight RGB and two multi-spectral datasets, using an automated object-based image analysis approach; (2) assess four traits, i.e., plant area, growth rates, condition and Plant Projective Cover (PPC) over the growing season; and (3) use the mapped traits to identify the best-performing accessions in terms of yield and salt tolerance. For the first five campaigns, >99% of all tomato plants were automatically detected. The omission rate increased to 2–5% for the last three campaigns because of the presence of dead and senescent plants. Salt-treated plants exhibited a significantly smaller plant area (average control and salt-treated plant areas of 0.55 and 0.29 m2, respectively), maximum growth rate (daily maximum growth rate of control and salt-treated plant of 0.034 and 0.013 m2, respectively) and PPC (5–16% difference) relative to control plants. Using mapped plant condition, area, growth rate and PPC, we show that it was possible to identify eight out of the top 10 highest yielding accessions and that only five accessions produced high yield under both treatments. Apart from showcasing multi-temporal UAV-based phenotyping capabilities for the assessment of plant performance, this research has implications for agronomic studies of plant salt tolerance and for optimizing agricultural production under saline conditions.