Excess sediment is one of the main agents of water pollution, affects the aquatic ecosystem and causes siltation problems in reservoirs and rivers. Bottom sediments are coarse and easily deposited, being the major responsible for morphological alterations in rivers. Therefore, is important to estimate the amount of sediment transported in other to establish mitigation strategies and recovery of affected areas. There are several methodologies for estimating bedload transport: equations, numerical modeling, direct physical sampling, and indirect method measuring dune tracking. Most studies measure bedload transport using the equipment Helley-Smith, generally taken as reference value for other methods. However, Helley-Smith causes changes in the flow field, often resulting in overestimates in sand bed rivers. Those overestimates were not yet described and quantified in detail. This article tries to solve this gap by observing the Helley-Smith sampler at the time of sampling. For this, we used a video camera recording processed by Particle Image Velocimetry (PIV) technique to qualitatively evaluate changes that the intrusive sampler causes in the displacement of bottom sediments in a sand bed river. When the sampler was properly allocated to the bottom, PIV resulting velocity maps of bedload particle transport identified the acceleration of the bottom particles as they approached the mouth of the sampler. We also noticed areas of convergence and vorticity of the sediments towards the sampler’s mouth, which may overestimate sampling. When the sampler’s mouth was disconnected from the bed due to the morphology of the bottom, we find regions of divergence in the displacement of the sediments creating unrealistic results for bedload transport analysis. In addition, the presence of organic matter can be underestimated, which causes difficulties in analyzing the quality of the collections because it is not possible to guarantee an equity in the positioning of the equipment at the bottom of the channel. We thus recommend complementation Helley-Smith measurements with surrogate methods, for example such as using ADCPs or optical methods, as the one described here.