The high productivity and efficiency of the use of irrigation water that characterizes greenhouse horticultural crops can be affected by poor irrigation distribution uniformity. The objective of this work was to estimate the average irrigation distribution uniformity (DU) of the greenhouses in Almería, determining the influence of the irrigation water quality as well as the production system on this uniformity. A prospective study was carried out in which commercial farms were selected that used different water qualities (groundwater vs. reclaimed) with different production systems (organic vs. conventional/integrated). The average irrigation distribution uniformity in the greenhouses of Almería was 80%. The farms with organic production systems presented a drastic DU reduction with respect to conventional farms (48% vs. 88%). The DU of the irrigation water presented in commercial farms irrigated with reclaimed water presented a lower DU than those irrigated with groundwater (76% vs. 86%). The distribution of irrigation depth of water in the greenhouses showed slight variations (from 3.2 to 2.9 mm) depending on the emitter position, with the highest values being at the head of the sub-main pipe and dripper line and the lowest at the end of the sub-main pipe and dripper line. The depth of water values was very close to the theoretical average of 3 mm. Water quality affects the distribution pattern of the depth of water in greenhouses. Installations irrigated with reclaimed water showed greater oscillation of the water depth within the sub-unit, varying from 3.6 to 2.0 mm, although the average depth was located close to the theoretical depth (3 mm). The production system affected the distribution of the depth of water—in the organic system, the depth underwent greater variation depending on the position of the emitter in the sub-unit, ranging from 1.7 to 3.3 mm. In addition, within this production system, the median depth of water was close to 2.5 mm, lower than the theoretical depth (3 mm), which denoted a certain generalized filling that was accentuated at the end of the dripper line and sub-main pipe.