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The environmental impacts of agricultural activities result from a chain of processes, agricultural practices affect the quantity and quality of natural resources, including biodiversity. Geographic information systems contribute to the systematic recording and monitoring of these agricultural practices in terms of production and to associate these practices with impacts on biodiversity. This paper presents the design of a web GIS system that records farming practices on a web map application (FarmGeoBalance), which is used by the farmers to import, store, revise and visualize farming practices in field level and farm level. The web map application communicates with a GeoDatabase informed with the geographical location of the participating fields where spatial and non-spatial data from the application are stored and standardized. The case study is an extensive arable farming system on Lemnos island, Greece, which covers a surface of 482 km². The system consists of 12 producers with 678 fields, representing 1.7% of the total farmed land of the island. In this paper, we present the web map application architecture and the collected data for the cultivation periods of 2020–2021 and 2021–2022, which include farming practices like fertilization, plant protection, irrigation, soil management, etc., outputs, landscape features of the farms related to biodiversity. For all these, their spatial and non-spatial dimension is presented and they are related to elements of the natural geography of fields and soils. With the use of this system recording and monitoring farming practices can assess the impact on biodiversity at multiple scales. It also highlights the need to include the end users at different phases of the development of the services and the interface. Farmers and their participation are the key component of the effectiveness of this effort: they monitor their everyday and seasonal practices at the level that they are realized in their farms.