The following database contains freshwater ostracode relative abundances from littoral and sediment surface samples of 76 aquatic ecosystems of the Northern Neotropical region. Samples were collected during July-October 2013, coinciding with the rainy season in the region. Sampling sites are located on the Yucatán Peninsula Mexico (n=28), Guatemala (n=26), El Salvador (n=14), Honduras (n=5) and Nicaragua (n=3). Ostracode species were used to test their potential as bioindicators of (paleo) climate change and anthropogenic impact in aquatic ecosystems of the region. At littoral areas, we sampled between submerged vegetation using a 250 µm mesh hand net, whereas sediment samples were collected from the deepest bottom using an Ekman grab. Ostracode extraction and counting was carried out using 15 cm3 of each sample. Species identification was undertaken using individual adult specimens with complete soft parts. When identification down the species level was not possible, we assigned a putative species name (e.g., “Cyprideis sp 1”).