Stable isotope techniques can help identify the sources of water pollution associated with agricultural activities. Knowing the origin of nutrients or contaminants is essential to improve agricultural practices. To ensure the quality of stable isotope analysis, appropriate sampling and sample preparation are crucial. This publication presents methods for surface water sampling and sample processing through micro-diffusion and bacterial denitrification combined with laser spectroscopy. Information on such methods is often described in a very summarized and non-comprehensive way without proper illustration of every step. This publication aims to bridge this gap for scientists, technicians and students. It presents a selection of standard operating procedures providing guidance in water sampling and sample preparation that are mandatory when conducting reliable isotope analysis on water.