Here, we present 23 water physical (temperature, dissolved oxygen, pH, conductivity) and chemical (major anions Cl-, SO42-, CO32-, HCO3- and cations Ca2+, K+, Mg2+, Na+), sedimentological (total carbon (TC), total inorganic carbon (TIC), total organic carbon (TOC), total nitrogen (TN)), mineralogical (quartz, carbonate, phyllosilicates and feldspars) and geological (altitude, bedrock type and age of sediments) variables of aquatic systems of the Northern Neotropical region. Sampling was conducted in 76 aquatic systems 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). We aim to identify limnological regions based on the measured variables and to infer the influence of geodiversity in observed patterns. Water physical and chemical variables were measured in situ with a WTW Multi Set 350i multiparameter probe at a water depth of 0.5 m. Water samples for analysis of major anions and cations were collected at water depths of 0.5 m below surface. TC and TN in sediments contents were determined by combustion with a LECO TruSpec Macro CHN analyzer. TIC was quantified with a Woesthoff Carmhograph C-16. TOC was calculated by subtracting TIC from TC. Qualitative and semi-quantitative mineralogical compounds were examined by x-ray diffraction with a RIGAKU Miniflex600. ArcGIS software was used to identify geological attributes of sampling sites such as bedrock and age of sediments. Altitude, latitude, and longitude were determined with the navigator Garmin GPSmap 60c.