The objective of this study was to describe the composition of two mesozooplankton and ichthyoplankton estuarine communities in Jandaíra, Bahia (Tabatinga River), impacted by a shrimp farm; and in Conde, Bahia (Itapicuru River), a pristine estuary. Samples were collected through horizontal hauls using a net (200 μm mesh size), coupled to a flowmeter, during the ebbing and flooding tides in April, August and December, 2007. In the Tabatinga and Itapicuru Rivers 76 and 92 taxa were registered. The most abundant groups were Pseudodiaptomus richardii and Disco sp. Acartia lilljeborgi was also dominant at Tabatinga, while Temora sp. and decapod larvae were predominant in Itapicuru River, which also presented higher densities for most planktonic taxa, particularly fish larvae. A descriptive analysis of the main taxa´s spatial distribution and new geographical records of Disco sp., P. richardi, Pontellopsis villosa, Macrosetella gracilis, Microsetella rosea, Gonyiopsillus brasiliensis, Agetus flaccus and Ergasilus caraguatatubensis were presented.