This datasets provides limnological data from three LTsER Montado stations (Heredade da Coitadinha, Heredade da Ribeira Abaixo, and Companhia das Lezhirias), both from the mapped waterbodies (AGROAQ_PHOTOINTERPRETATION_WATERBODIES_2024), and from the surveyed ponds and troughs (AGROAQ_FIELD_SAMPLING_DATA_2024). Data from mapped waterbodies include the location, tipology (pond or trough) and the hydroperiod. Data from the field surveys include physichochemical, morphological, and other variables, such as chlorofil-a concentration, and macroinvertebrates and macrophytes presence/absence. This project starts the first attempt to date, to start a limnological monitoring on this LTER Montado.