This dataset was developed during the NATMed project (PRIMA Programme, supported by the European Union under Grant Agreement No. 2221) and is jointly owned by CARTIF and AMAYA under a CC-BY 4.0 license. It compiles ecological monitoring data collected at the CS1 site (Experimental Centre for New Water Technologies) located in Carrión de los Céspedes, Spain. The dataset consists of two complementary Excel files. The first file contains chlorophyll-a concentration measurements (µg/L), obtained using spectrophotometric analysis, as an indicator of trophic status and water quality. Associated variables include sampling point (categorical), sampling date (dd/mm/yyyy), sampling month (categorical), and sampling year (categorical), providing temporal and spatial context for each observation. The second file includes biodiversity observations used as bioindicators to assess ecological status and ecosystem health. This file contains species-level information such as scientific name (taxonomic identification), type (native or non-native), and annual occurrence (presence/absence, where 1 indicates presence and 0 absence). The data are provided in .xlsx format, with additional supporting materials including photographic records of identified species (JPEG format) and georeferenced data (KMZ format) for species identified in 2025.