The article presents a study to substantiate approaches to the integrated use of information technologies for environmental monitoring tasks in the concept of an ecosystem as a complex organizational system for the functioning of a smart city (region). The results of monitoring water resources as an element of the ecosystem are presented. The task of timely detection of anthropogenic impact on water resources is relevant in the concept of ensuring the functioning of regional ecosystems in accordance with certain safety standards to prevent negative impacts on human health and ecology of the region. The main requirements for the model are related to the following indicators: the scale of monitoring; discreteness of information; accuracy of the parameters to be monitored; adaptability of the monitoring system. The information technologies proposed for integration include: geographic information system technologies based on remote sensing data, information technologies for ensuring the functioning of the air component in the performance of monitoring tasks based on the use of unmanned aerial vehicles, information technologies for the primary level of monitoring data collection based on the deployment of a sensor network. The theoretical provisions presented in the article are confirmed by empirical research. The presented approaches can be considered as ways to improve the efficiency of the decision support system in the concept of ensuring the functioning of the region’s ecosystem.