Clogging of gravel-bed rivers is a major issue for fish and macro-invertebrate habitats as well as for groundwater-river exchanges. River clogging consists mainly of the deposition and infiltration of fine sediments within the bed matrix, which is a natural phenomenon but can be enhanced by human activities. Although there are several methods for estimating the degree of clogging, quantitative assessment of clogging remains challenging, not to mention the lack of comparison between these methods. We therefore implemented three quantitative methods for estimating clogging (bed material sampling, infiltration test, and interstitial water sampling), and assessed their effectiveness and suitability for application as a long-term monitoring solution. These methods were applied to a natural river bed characterised by high spatial heterogeneity of clogging. The results show good correlations between the different methods despite some scatter that can be linked to limitations of some methodologies in term of sampling itself or sampling depth. Indeed, sampling of the bed material using a McNeil sampler is limited to the first 15 cm below the surface, whereas the infiltration test or interstitial water pumping using a standpipe can be achieved for a depth deeper than 15 cm only. The infiltration test appears to be effective for relatively low clogging, while interstitial water sampling is more efficient for high clogging. The results also show that dissolved oxygen estimation alone may not be sufficient to accurately estimate physical clogging, particularly for cases of low clogging. However, it appears to be a good and simple complementary method to the interstitial water-sediment pumping method. The infiltration test and interstitial water-sediment sampling are simple, quick and easy to apply methods. The two methods are complementary, and suitable for a spatial clogging assessment, with the possibility of investigating a wide range of clogging degrees.