Morphological abnormalities in crustaceans have been registered and several are attributed to pollution and others anthropogenic activities. This study reports for the first time a temporal record of the amount and variety of morphological abnormalities in Acartia lilljeborgii, in an impacted neotropical estuary. The specimens were obtained from Suape port area, Northeast Brazil, between May 2009 and September 2010 using a 300 µm plankton net. Seven types of abnormalities were observed in one of the terminal spines of the prosome, but no temporal variation of abnormalities was found in our study. The deformities were registered in 85.7% of samples and they were found in up to 10% of the individuals (3.2 ± 2.9%). The proportion of females with abnormalities was greater than for males, in opposite to most previous reports. Due to its high distribution and abundance in part of the neotropical Atlantic coastal area, A. lilljeborgii has the potential to be used as a bioindicator of environmental conditions, although the reasons of the abnormality occurrences should be accurately investigated.