The high organic load of the effluent generated in these farms has an important environmental impact, which is amplified in insular or isolated territories. The application of natural treatment systems of wastewater (NTSW) has demonstrated their suitability in these environments, but their design lacks proper characterization and sizing tools for their adequate operation. This work proposes a series of strategies and tools for the design and characterization of NTSW. As an application, an inventory, characterization, sizing, and design is carried out in 9 pig farms with a high environmental impact located on the island of Gran Canaria (Spain). The proposed tools in this work are based on a collection of experimental data over a five-year period of application of NTSW in real farms. This work contributes to facilitate the design and implementation of NTSW in farms located in isolated, island or similar size environments.