Because of their fast response to hydrological events, small catchments show strong quantitative and qualitative variations in their water runoff. Fluxes of solutes or suspended material can be estimated from water samples only if an appropriate sampling scheme is used. We used continuous in-stream measurements of the electrical conductivity of the runoff in a small subalpine catchment (64 ha) in central Switzerland and in a very small (0.16 ha) subcatchment. Different sampling and flux integration methods were simulated for weekly water analyses. Fluxes calculated directly from grab samples are strongly biased towards high conductivities observed at low discharges. Several regressions and weighted averages have been proposed to correct for this bias. Their accuracy and precision are better, but none of these integration methods gives a consistently low bias and a low residual error. Different methods of peak sampling were also tested. Like regressions, they produce important residual errors and their bias is variable. This variability (both between methods and between catchments) does not allow one to tell a priori which sampling scheme and integration method would be more accurate. Only discharge-proportional sampling methods were found to give essentially unbiased flux estimates. Programmed samplers with a fraction collector allow for a proportional pooling and are appropriate for short-term studies. For long-term monitoring or experiments, sampling at a frequency proportional to the discharge appears to be the best way to obtain accurate and precise flux estimates.