Protected cultivation is gaining momentum in (semi) arid regions to ameliorate the adverse environmental impacts on vegetable crops, besides ensuring high resource use efficiency in resource-limiting environments. Among the less techno-intensive protected cultivation structures, naturally ventilated polyhouses (NVP), insect-proof net houses (IPN) and shade net houses (SNH) are commercial structures in India. With the aim to find the best-protected structure, together with optimum irrigation level, for high yield and water productivity of the tomato crop, the most popular crop in hot arid regions, we evaluated tomato performance in low-tech protected structures (NVP, IPN and SNH) in interaction with three irrigation levels (100, 80 and 60% of crop evapotranspiration, ETc) during spring–summer of 2019 and 2020. The NVP was found superior to both the net house structures (IPN and SNH) for different performance indicators of tomatoes under investigation. The components of plant growth (leaf and stem dry mass) and fruit yield (fruit size, weight, yield), as well as fruit quality (total soluble solids, fruit dry matter and lycopene content) were higher in NVP, regardless of irrigation level. The yield as well as water productivity were significantly higher in NVP at 100% ETc. However, there was no statistical variation for water productivity between NVP and IPN. Microclimate parameters (temperature, relative humidity and photosynthetic active radiation) were markedly more congenial for tomato cultivation in NVP followed by IPN in relation to SNH. Consequently, plants’ physiological functioning with higher leaf relative water content (RWC) and lower leaf water potential concomitantly with better photosynthetic efficiency (chlorophyll fluorescence, F_v/F_m), was in NVP and IPN. Most growth and yield attributes were depressed with the decrease in water application rates; hence, deficit irrigation in these low-tech protected structures is not feasible. For tomato cultivation in resource-scarce arid regions, the combination of the normal rate of irrigation (100% ETc) and NVP was optimal for gaining high yield as well as water productivity as compared to net houses.