The heterotrophic ciliates, mainly composed of aloricate (naked) ciliates, are the dominant size fraction and play an important role in low impacted subtropical coastal systems of central region of the Gulf of California, México, by consuming up to 70% of phytoplankton biomass (pico- and nanoplankton). However, there is no information concerning microzooplankton populations for lagoons highly impacted by anthropogenic activities. This study established a baseline of regional abundance and spatio-temporal variability of aloricate ciliates and tintinnids, in the eutrophic lagoon system Topolobampo-Santa María-Ohuira. Their total abundance ranged from 10 to 56.1×103 org L−1 for ciliate, and 10 to 14.80×103 org L−1 for tintinnids. Aloricate ciliates mean abundances were approximately four times higher than that of tintinnids, with higher values occurring in winter–spring and punctuated by minor spurts during the rainy months. The study found that eutrophication levels (6.5 to 7.3 TRIX units) were the main factor contributing to their abundance, though tropic interactions and lagoon hydrological characteristics were also relevant. Their distribution revealed that substantial population increases resulted from nutrient enriched residual agricultural drainage at Santa María and Ohuira that exacerbated eutrophication conditions. Canonical correspondence analysis identified that lower values of salinity was due to the influence of wastewater effluent discharge and was the main variable that was related with tintinnids; while dissolved oxygen and chlorophyll-a, variables associated to large primary production, were related to ciliates. The deteriorated water quality of Santa María and Ouhira lagoons likely delineated the low macro-zooplanktonic biomasses and consequently the higher aloricate ciliates and tintinnids abundances.