Reservoirs are dynamic ecosystems subject to different pressures that influence and compromise their ecological structure. The main objective of this study was to evaluate the potential of using the macroinvertebrate to assess the water quality of four reservoirs (one site in Miranda—M and Pocinho—P; four sites in Aguieira—Ag1 to Ag4; and five sites in Alqueva—Al1 to Al5). The sites were sampled in autumn 2018 (A18), spring and autumn 2019 (S19 and A19) and spring 2020 (S20). In situ physical and chemical parameters were measured and a sample of water and macroinvertebrate were collected for further analyses. Total phosphorus exceeded the allowed concentrations (maximum values recorded: M—0.13 mg/L, P—0.09 mg/L, Ag3—0.22 mg/L and Al5—0.18 mg/L). Total abundance varied between 4 and 3088. Taxonomic richness was always low, between 1 and 12 taxa. The highest Shannon–Wiener value (1.91) was recorded in Ag1_A18 and Al2_A18. Pielou’s evenness varied widely across all reservoirs, from 0.06 to 0.92. Almost all the organisms found were associated with polluted water, according to the index ratings. Organisms tolerant of disturbances (e.g., Chironomidae and Oligochaeta) were associated with sites with the worst water quality, according to the Water Framework Directive (WFD), (M, Ag3, Ag4 and Al5) while organisms with moderate tolerance to disturbances (e.g., Cordullidae and Polycentropodidae) were associated with sites with better water quality (P, Ag1, Ag2 and Al1 to Al4). The macrozoobenthos index (MZB) used proved to be a sensitive tool to Portuguese reservoirs, corroborating most of the results obtained in the remaining analyses, as well as providing a clear ecological potential complementing the analysis carried out by the WFD. Based on this, the macroinvertebrate community appeared to be sensitive and able to characterize the reservoirs’ water quality.