Land cover evolution is an environmental factor that can be used to characterize forest ecosystem services (FES). This study aims to analyze the change in forest cover and water bodies between 1990 and 2018 in the whole Czech Republic, and in the Central Bohemian and South Moravian regions, and its effects on freshwater provision. Additionally, we attempt to understand the societal implications of water quality, public perception, and environmental investment on natural ecosystems. Forest cover and water body data were obtained from the Corine land cover database, while water quality and investment were compiled from the Czech Statistical Office. Public perceptions on the Czech FES were collected from a national survey. Between 1990 and 2018, forest cover has increased by 3.94% and water bodies by 7.65%; however, from 2014 to 2018, severe droughts were reported that compromised the availability of surface water, presumably on artificial structures, causing an increase in the occupied area. Regarding public perception, respondents with less education, and the older population, obtained an assessment of the low performance of the FES, while the water quality and investment indicate that environmental funding has contributed to improving the quality of outflow water from the wastewater treatment plants, fulfilling all the allowed limits of the urban wastewater treatment directive. Hence, a multidisciplinary approach can help decision makers promote policies that integrate environmental management measures, investment protection, and contribute to sustainable development.