Climate change has reduced the availability of good quality water for agriculture, while favoring the proliferation of harmful insects, especially in Mediterranean areas. Deploying IoT-based systems can help optimize water-use efficiency in agriculture and address problems caused by extreme weather events. This work presents an IoT-based monitoring system for obtaining soil moisture, soil electrical conductivity, soil temperature and meteorological data useful in irrigation management and pest control. The proposed system was implemented and evaluated for olive parcels located both at coastal and inland areas of the eastern part of Crete; these areas face severe issues with water availability and saltwater intrusion (coastal region). The system includes the monitoring of soil moisture and atmospheric sensors, with the aim of providing information to farmers for decision-making and at the future implementation of an automated irrigation system, optimizing the use of water resources. Data acquisition was performed through smart sensors connected to a microcontroller. Data were received at a portal and made available on the cloud, being monitored in real-time through an open-source IoT platform. An e-mail alert was sent to the farmers when soil moisture was lower than a threshold value specific to the soil type or when climatic conditions favored the development of the olive fruit fly. One of the main advantages of the proposed decision-making system is a low-cost IoT solution, as it is based on open-source software and the hardware on edge devices consists of widespread economic modules. The reliability of the IoT-based monitoring system has been tested and could be used as a support service tool offering an efficient irrigation and pest control service.